US20180265524A1

US20180265524A1 - Small molecules for the modulation of mcl-1 and methods of modulating cell death, cell division, cell differentiation and methods of treating disorders

Info

Publication number: US20180265524A1
Application number: US15/968,384
Authority: US
Inventors: Loren D. Walensky; Michelle L. Stewart; Nicole Cohen
Original assignee: Dana Farber Cancer Institute Inc
Current assignee: Dana Farber Cancer Institute Inc
Priority date: 2010-01-29
Filing date: 2018-05-01
Publication date: 2018-09-20
Also published as: WO2011094708A2; EP2528893A4; AU2011210567B2; WO2011094708A3; AU2011210567A1; EP2528893B1; JP2013518816A; US20150315211A1; JP2016183175A; US20130035304A1; JP6227707B2; US10000511B2; EP3138838A1; EP2528893A2; JP5937968B2; CA2787784A1

Abstract

This invention relates to compounds which selectively bind to the survival protein MCL-1 with high affinity and selectivity, pharmaceutical compositions containing such compounds and the use of those compounds or compositions for modulating MCL-1 activity and for treating hyperproliferative disorders, angiogenesis disorders, cell cycle regulation disorders, autophagy regulation disorders, inflammatory disorders, and/or infectious disorders and/or for enhancing cellular engraftment and/or wound repair, as a sole agent or in combination with other active ingredients.

Description

This application is a divisional and claims priority of co-pending U.S. application Ser. No. 14/705,764, filed May 6, 2015, which is a divisional of U.S. application Ser. No. 13/576,116, filed Jul. 30, 2012 and having a 371 completion date of Oct. 22, 2012, now abandoned, which is a U.S. National Stage application, and claims priority of International Application No. PCT/US2011/023220, filed Jan. 31, 2011, which claims priority of U.S. Provisional Application Ser. No. 61/299,803, filed Jan. 29, 2010. The contents of all of the prior applications are incorporated herein by reference in their entirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under grant number P01CA92625 awarded by The National Institutes of Health. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Beginning with the discovery of BCL-2 at the t14;18 chromosomal breakpoint of follicular lymphoma^1-3, the anti-apoptotic members of the BCL-2 family have emerged as key pathogenic proteins in human diseases characterized by unchecked cellular survival, such as cancer and autoimmunity. A series of anti-apoptotic proteins including BCL-2, BCL-X_L, BCL-w, MCL-1, BFL1/A1, and BCL-B promote cellular survival by trapping the critical apoptosis-inducing BCL-2 homology domain 3 (BH3) α-helix of pro-apoptotic BCL-2 family members⁴. Cancer cells exploit this physiologic survival mechanism through anti-apoptotic protein overexpression, establishing an apoptotic blockade that secures their immortality. To overcome this potentially fatal resistance mechanism, a pharmacologic quest is underway to develop targeted therapies that bind and block BCL-2 family survival proteins.
Anti-apoptotic proteins contain a hydrophobic binding pocket on their surface that engages BH3 α-helices^4,5. Because Nature's solution to anti-apoptotic targeting involves selective interactions between BH3 death domains and anti-apoptotic pockets^6,7, molecular mimicry of the BH3 α-helix has formed the basis for developing small molecule modulators of anti-apoptotic proteins^8-10. Promising compounds undergoing clinical evaluation, such as ABT-263¹¹, obatoclax⁹, and AT-101¹², each target three or more anti-apoptotic proteins. The development of more precise inhibitors that target individual anti-apoptotic proteins remains a significant challenge due to the often subtle differences among BH3-binding pockets. Reminiscent of the long-term goals in kinase therapeutics, anti-apoptotic inhibitors with greater specificity would provide finely-tuned therapies to treat distinct diseases while potentially avoiding unwanted side-effects, such as those observed for ABT-263¹¹and AT-101¹³. In addition, such compounds would serve as invaluable research tools to dissect the differential biological functions of anti-apoptotic proteins.
The specificity of anti-apoptotic proteins for BH3 domains is conferred by the topography of the canonical binding groove and the distinctive amino acid composition of the interacting BH3 helix. Whereas some BH3 domains, such as that of pro-apoptotic BIM, can tightly engage all anti-apoptotic pockets, others are more selective like the BAD BH3 that binds BCL-2, BCL-X_L, and BCL-w and the NOXA BH3 that targets MCL-1 and BFL1/A1⁶. The differential binding capacity of BH3 domains and their mimetics is clinically relevant, as exemplified by the close relationship between inhibitor binding spectrum and biological activity. For example, ABT-737, the prototype small molecule BH3 mimetic modeled after the BH3 domain of BAD, was designed to specifically target BCL-2 and BCL-X_L ¹⁰, and induces apoptosis in select cancers that are driven by these proteins^14-16. However, ABT-737 fails to show efficacy against cancer cells that overexpress MCL-1, as this anti-apoptotic lies outside the molecule's binding spectrum^15-17. In an effort to overcome the challenge of designing precision small molecules to selectively target interaction surfaces that are comparatively large and more complex, we investigated whether Nature's selective BH3 domains could be used to rapidly identify precise small molecule modulators.
The development of precise inhibitors for discrete anti-apoptotic BCL-2 family proteins implicated in pathologic cell survival remains a formidable but pressing challenge. Such compounds would provide finely-tuned molecular probes to study and treat human diseases driven by specific anti-apoptotic blockades. For example, anti-apoptotic MCL-1 has emerged as a major resistance factor in cancer.
MCL-1 overexpression has been linked to the pathogenesis of a variety of refractory cancers, including multiple myeloma^18,19, acute myeloid leukemia¹⁶, melanoma²⁰, and poor prognosis breast cancer²¹. MCL-1 exerts its pro-survival activity at the mitochondrial outermembrane where it neutralizes pro-apoptotic proteins such as NOXA, PUMA, BIM, and BAK. The critical role of MCL-1 in selective apoptotic resistance has been highlighted by the sensitizing effects of small interfering RNAs that downregulate MCL-1 protein levels^22,23.
Despite the formidable challenges associated with developing precise small molecule modulators of biomedically relevant protein targets, the identification of novel and selective small molecules modulators of MCL-1 is described herein.

BRIEF SUMMARY OF THE INVENTION

One embodiment of this invention encompasses a compound of the formula:

Wherein:

X is ═O or —O—R³;
R¹is substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloallcyl, —S—R^2a, —SO₂R^2a;
R²is hydrogen, halogen, —O—R^2a, —NH—R^2a, —S—CN, —S—R^2a, —S—CH²—R^2aor —SO₂R^2a;
R^2ais C₁-C₈alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl;
and R³is hydrogen, C₁-C₈alkyl substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl; or

Wherein:

R⁴and R⁵are independently hydrogen, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloallcyl, or substituted or unsubstituted heterocycloalkyl or are taken together to form a 5-7 membered, optionally substituted, heteroaryl or heterocycloalkyl, provided that no more than one of R⁴and R⁵is hydrogen;
And R⁶is substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloallcyl, or substituted or unsubstituted heterocycloalkyl; or

Wherein:

R⁷is CH2-CO—R^7a; —CH₂—NH—SO₂—R^7a;
and R^7ais substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl; or

Wherein:

R⁸is —CO—R^8a; —CO—NH—(CH₂)_n—R^8a; —CO—CH₂—R^8a, —NH—CO—NH—R^8a; —NH—SO₂—NH—R^8a; or —NH—CO—R^8a; —NH—SO₂—R^8a
and R^8ais substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloallcyl, or substituted or unsubstituted heterocycloalkyl; or

Wherein

- R⁹is hydrogen, C₁-C₆alkyl, C₂-C₆alkeynyl, C₂-C₆alkynyl, —NH₂, —NHR^9a, —NR^9aR^9b, —COH, —COR^9a, —COOH, or —COOR^9a;

R^9aand R^9bare independently C₁-C₆alkyl, C₂-C₆alkeynyl, C₂-C₆alkynyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloallcyl, or substituted or unsubstituted heterocycloalkyl
W is
—R¹⁰,
—CO—R¹⁰,
—CO—(CH₂)_n—R¹⁰,
—CO—NH—R¹⁰,
—CO—NH—(CH₂)_n—R¹⁰,
—CO—NH—CO—NH—(CH₂)_n—R¹⁰,
—CO—NH—SO—NH—(CH₂)_n—R¹⁰,
—SO—(CH₂)_n—R¹⁰,
—SO—NH—(CH₂)_n—R¹⁰,
—SO—NH—CO—NH—(CH₂)_n—R¹⁰,
—SO—NH—SO—NH—(CH₂)_n—R¹⁰, or
the group
wherein * represents the point of attachment;
R¹⁰is Z or substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl;
R¹²is Z or hydrogen, C₁-C₆alkyl or —(CH₂)_n—R^12a,
R^12ais Z or substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl; or

Wherein

R¹³is C₁-C₈alkyl, C₂-C₈alkenyl, C₂-C₈alkynyl, or C₁-C₆alkoxy,
and R¹⁴is substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl wherein R¹⁴may be further substituted by Z; or

Wherein

R15 is hydrogen, hydroxyl, halogen, —CO—(CH₂)_n—R^15a, —CO—NH—(CH₂)_n—R^15a, —CO—NH—CO—NH—(CH₂)_n—R^15a, —CO—NH—SO—NH—(CH₂)_n—R^15a, NH—CO—(CH₂)_n—R^15a, NH—CO—NH—(CH₂)_n—R^15a, —SO—(CH₂)_n—R^15a, —SO—NH—(CH₂)_n—R^15a, —SO—NH—CO—NH—(CH₂)_n—R^15a, —SO—NH—SO—NH—(CH₂)_n—R^15a, or —NH—SO₂—R^15a; alkyl C1-C8-R15a
R^15ais substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl;
and R¹⁶is hydrogen, halogen, hydroxyl or substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl; or

Wherein

X is O or S;
R¹⁷is substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl, wherein R¹⁷may be further substituted by Z;
R¹⁸is hydrogen, C₁-C₈alkyl, C₂-C₈alkenyl, C₂-C₈alkynyl, or C₁-C₆alkoxy, wherein R¹⁸may be further substituted by Z;
and R¹⁹is hydrogen, C₁-C₈alkyl, C₂-C₈alkenyl, C₂-C₈alkynyl, or C₁-C₆alkoxy wherein R¹⁹may be further substituted by Z; or

Wherein

Y¹is N, NH, CH or CH₂;
Y²is O, S, or NH;
- - - represents an optional double bond;
R²⁰is substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl, wherein R²⁰may be further substituted by Z;
R²¹represents ═S, ═NH, —NHR^R2a, —CHR^21a, ═NR—^21a, or ═CCO—R^21a; and
R^21ais substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl, wherein R^21amay be further substituted by Z; or

Wherein

R²²is substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl wherein R²²may be further substituted by Z;
R²³is C₁-C₈alkyl, C₂-C₈alkenyl, C₂-C₈alkynyl, or C₁-C₆alkoxy, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl wherein R²³may be further substituted by Z; and
R²⁴is C₁-C₈alkyl, C₂-C₈alkenyl, C₂-C₈alkynyl, or C₁-C₆alkoxy, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloallcyl, or substituted or unsubstituted heterocycloalkyl wherein R²⁴may be further substituted by Z; or

Wherein

R²⁵is —CO—R^25a; —CO—NH—(CH₂)_n—R^25a; —CO—CH₂—R^25a, —NH—CO—NH—R^25a; —NH—SO₂—NH—R^25a; or —NH—CO—R^25a; —NH—SO₂—R^25a
R^25ais substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl wherein R²²may be further substituted by Z; or

Wherein

R²⁶is substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl wherein R²²may be further substituted by Z; or
and wherein
in each of formulas A-L:
each occurrence of n is independently an integer from 0-4;
each occurrence of m is independently an integer from 0-3;
each occurrence of p is independently an integer from 0-2;
each occurrence of q is independently an integer from 0-1;
each occurrence of Z, Z′ and Z″ is independently halogen, hydroxyl, C₁-C₈alkyl, C₂-C₈alkenyl, C₂-C₈alkynyl, or C₁-C₆alkoxy, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl,
or M)
a compound having the formula
T¹L-T²_uQ-T²

Wherein:

T¹represents a compound of the formula A-L;
each T²independently represents another compound of the formula A-L which may be the same or different from T¹;
each Q represents a direct bond, a C₁-C₈alkylene linker, a C₂-C₈alkenylene linker, a C₂-C₈alkynylene linker, an amide linker, or a sulfonamide linker formed by joining together a Z, Z′, or Z″ moiety of T¹with a Z, Z′, or Z″ moiety of each subsequent T²; and
u represents an integer from 0-5
or a pharmaceutically acceptable salt, solvate, hydrate or stereoisomer thereof.
In some embodiments, the invention encompasses a compound of having the formula M:
T¹L-T²_uQ-T²

Wherein:

T¹represents a compound of the formula A-L;
each T²independently represents another compound of the formula A-L which may be the same or different from T¹;
each Q represents a direct bond, a C₁-C₈alkylene linker, a C₂-C₈alkenylene linker, or a C₂-C₈alkynylene linker formed by joining together a Z, Z′, or Z″ moiety of T¹with a Z, Z′, or Z″ moiety of each subsequent T²; and
u represents an integer from 0-5
or a pharmaceutically acceptable salt, solvate, hydrate or stereoisomer thereof.
In some embodiments, the invention encompasses a compound having the formula M wherein u is 0 and Q is a direct bond.
In still other embodiments, the invention encompasses a compound having the formula M wherein u is 0 and Q is a C₁-C₈alkylene linker.
In yet other embodiments, the invention encompasses a compound having the formula M wherein u is 1 and each Q is independently a direct bond or a C₁-C₈alkylene linker.
Representative compounds and subclasses of compounds of the invention are identified in Table 1 (including Subtables Table 1-A through Table 1-P). These compounds may be useful in the methods and compositions described herein.
Another aspect of the invention encompasses a pharmaceutical composition comprising one or more compounds according to Formula A-M or physiologically acceptable salts, solvates, hydrates, stereoisomers, or fusion compounds thereof and a pharmaceutically acceptable diluent or carrier. In some embodiments, the pharmaceutical composition the invention encompasses a composition wherein the compound is present in a therapeutically effective amount.
In still another embodiment, the pharmaceutical composition the invention, further encompasses at least one further active compound. In one embodiment, the further active compound is a death receptor stimulant, an HDAC inhibitor, a proteasome inhibitor, a BCL-2 family inhibitor, a kinase inhibitor, a mitotic inhibitor, a nucleoside analog, an anti-cancer monoclonal antibody, a corticosteroid, a DNA-damaging agent, an antimetabolite, or other cell death-activating stimulant.
Another aspect of the invention encompasses a packaged pharmaceutical composition comprising a container, the pharmaceutical composition of the invention and instructions for using the pharmaceutical composition to treat a disease or condition in a mammal.
Yet another aspect of the invention encompasses a method of modulating MCL-1 in a cell comprising contacting a cell with one or more compounds of the invention. In one embodiment, the activity modulated is apoptotic cell death. In another embodiment, the activity modulated is autophagy. In another embodiment, the activity modulated is necrotic cell death. In another embodiment, the activity modulated is cell metabolism. In another embodiment, the activity modulated is cell division. In another embodiment, the activity modulated is transcription in a cell. In another embodiment, the activity modulated is RNA Processing in a cell. In another embodiment, the activity modulated is cell differentiation. In another embodiment, the activity modulated is transcription. In another embodiment, the activity modulated is RNA processing. In another embodiment, the activity modulated is protein multimerization or dissociation.
Still another aspect of the invention encompasses a method of treating a hyperproliferative disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention. In some embodiments, the hyperproliferative disorder is cancer, including but not limited to, cancer of the breast, respiratory tract, brain, reproductive organs, digestive tract, urinary tract, eye, liver, skin, head and neck, thyroid, parathyroid or a distant metastasis of a solid tumor, a lymphoma, sarcoma, melanoma or leukemia.
Yet another aspect of the invention encompasses a method of treating an angiogenesis disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Still yet another aspect of the invention encompasses a method of treating an inflammatory disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Another aspect of the invention encompasses a method of treating an infectious disease in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Still another aspect of the invention encompasses a method of treating a cell cycle regulation disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Yet another aspect of the invention encompasses a method of treating an autophagy regulation disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Still yet another aspect of the invention encompasses a method of treating an autoimmune disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Another aspect of the invention encompasses a method of enhancing wound repair in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Yet another aspect of the invention encompasses a method of enhancing cellular engraftment in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Another aspect of the invention encompasses a method of sensitizing a cell to treatment by a secondary active ingredient comprising administering to a cell a sensitizing amount of one or more compounds of the invention. In certain embodiments, the secondary active ingredient is a death receptor stimulant, an HDAC inhibitor, a proteasome inhibitor, a BCL-2 family inhibitor, a kinase inhibitor, a mitotic inhibitor, a nucleoside analog, an anti-cancer monoclonal antibody, a corticosteroid, a DNA-damaging agent, an antimetabolite, or other cell death-activating stimulant.
It is noted that in this disclosure and particularly in the claims and/or paragraphs, terms such as “comprises”, “comprised”, “comprising” and the like can have the meaning attributed to it in U.S. Patent law; e.g., they can mean “includes”, “included”, “including”, and the like; and that terms such as “consisting essentially of” and “consists essentially of” have the meaning ascribed to them in U.S. Patent law, e.g., they allow for elements not explicitly recited, but exclude elements that are found in the prior art or that affect a basic or novel characteristic of the invention. These and other embodiments are disclosed or are obvious from and encompassed by, the following Detailed Description.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A shows the application of a selective stapled peptide in a competitive binding screen to identify selective small molecules against a protein target.

FIG. 1B shows workflow for identifying small molecules that selectively target MCL-1.

FIG. 2A shows a surface view of the BH3-binding pocket of MCL-1ΔNΔC from the X-ray structure of MCL-1 (PDB ID: 2PQK), with discrete topographic regions of the binding surface labeled A-E.

FIG. 2B shows examples of selective small molecule binders of MCL-1ΔNΔC engaging discrete topographic regions (labeled A-E) of the BH3-binding pocket, as rendered by molecular docking. Since certain small molecules cover distinct regions of the pocket, synthetic combinations of molecules or fragments thereof can yield a larger molecule that selectively binds a greater surface area of the BH3-binding pocket. The identified topographic coverage of select molecules include compounds 1, (A+B); 2, (B+C); 3, (C+D); 4, (A+E); 5, (A+B+C); 6, (E+B+C).

FIG. 2C shows the results of a dilutional assay that revealed selective small molecule binders can be subclassified based on engaging MCL-1 through noncovalent or covalent interactions. FITC-BID BH3 binding to MCL-1 is restored upon dilution in the top panel (molecule 1570G15), whereas competitive FITC-BID BH3 binding cannot be restored by dilution once MCL-1 is exposed to small molecules 1725P16 and 1579E07. These data suggest that 1570G15 engages MCL-1 through non-covalent interactions, whereas 1725P16 and 1579E07 covalently modify MCL-1, preventing re-engagement by FITC-BID BH3 even after protein dilution.

FIG. 2D shows that a subgroup of MCL-1 inhibitor molecules covalently reacted with C286 of MCL-1 at a novel interaction site. Proteomic analysis determined that a subset of molecules that covalently modify MCL-1 react at C286 of the identified tryptic fragment, revealing a discrete binding site for MCL-1 that differs in location from the canonical BH3 binding site engaged by MCl-1 SAHB.

FIG. 2E demonstrates that C286S mutagenesis abrogates binding of this subgroup of molecules, confirming engagement of a novel interaction site for MCL-1 inhibition. Molecules that covalently modify MCL-1 at C286 (1929A19; 161N08 [Class A]) effectively block FITC-BID BH3 binding to MCL-1. This small molecule activity is specifically abrogated by C286S mutagenesis, implicating interactions at a novel site in the modulation of binding activity at the canonical BH3 binding pocket of MCL-1.

FIG. 3A shows the degree of MCL-1 selectively as determined by competitive fluorescence polarization binding assays (FPA) in a secondary screen of small molecule hits from a bioactive library against FITC-BID BH3/anti-apoptotic protein interactions.

FIG. 3B demonstrates that small molecule bioactives identified as MCL-1 selective indeed exhibit preferential displacement of FITC-BID BH3 from MCL-1ΔNΔC compared to other anti-apoptotic proteins. The tabulated IC₅₀values are shown.

FIG. 4A shows the degree of MCL-1 selectivity as determined by competitive fluorescence polarization binding assays (FPA) in a secondary screen of hits from small molecule libraries against FITC-BID BH3/anti-apoptotic protein interactions. Competitive FPA binding curves as shown.

FIG. 4B shows tabulated IC50 values in μM, demonstrating that small molecules identified as MCL-1 selective exhibit preferential displacement of FITC-BID BH3 from MCL-1ΔNΔC compared to other anti-apoptotic proteins.

FIG. 4C shows structure-activity relationship (SAR) analysis for select derivatives of Class A molecular inhibitors of MCL-1, using the FITC-BID BH3/MCL-1ΔNΔC competitive fluorescence polarization binding assay.

FIG. 4D shows structure-activity relationship (SAR) analysis for select derivatives of Class J molecular inhibitors of MCL-1, using the FITC-BID BH3/MCL-1ΔNΔC competitive fluorescence polarization binding assay.

FIG. 5A shows that a SAHB peptide selective for MCL-1 sensitizes TRAIL-induced and caspase-dependent cell death of Jurkat T-cell leukemia and OPM2 multiple myeloma cells. MCL-1-targeting small molecule hits synergize with TRAIL to induce cell death of OPM2 cells.

FIG. 5B shows that small molecule bioactives that target MCL-1 also sensitize the capacity of TRAIL to inhibit viability of OPM2 cells, as has been shown for selective targeting of MCL-1 with MCL-1 SAHB (FIG. 5A) and for selective knock-down of MCL-1 with siRNA.

FIG. 5C shows a combination treatment analysis using CalcuSyn software revealing combination index values that reflect synergy between treatment with TRAIL and the identified small molecule bioactive hits that target MCL-1. The tabulated combination index values document synergy of MCL-1-targeting molecules from bioactive library in reducing OPM2 cell viability when combined with TRAIL.

FIG. 5D shows a combination treatment analysis using CalcuSyn software revealing combination index values that reflect synergy between treatment with TRAIL and the identified small molecule hits that target MCL-1. The tabulated combination index values document synergy of MCL-1-targeting molecules from small molecule libraries in reducing OPM2 cell viability when combined with TRAIL. (CI<0.9, synergy; 0.9<CI<1.1, additive effect; CI>1.1, antagonism).

FIG. 6 shows that selective MCL-1 inhibitor molecules block the anti-apoptotic activity of MCL-1 in a BAX-mediated liposomal release assay. MCL-1 blockade of tBID-induced, BAX-mediated liposomal release is inhibited by pretreatment of MCL-1 with the selective small molecule MCL-1 inhibitors.

DETAILED DESCRIPTION OF THE INVENTION

Definitions

In order that the invention may be more readily understood, certain terms are first defined and collected here for convenience. Other definitions appear in context throughout the application.
In this disclosure, “comprises,” “comprising,” “containing” and “having” and the like can have the meaning ascribed to them in U.S. Patent law and can mean “includes,” “including,” and the like; “consisting essentially of” or “consists essentially” likewise has the meaning ascribed in U.S. Patent law and the term is open-ended, allowing for the presence of more than that which is recited so long as basic or novel characteristics of that which is recited is not changed by the presence of more than that which is recited, but excludes prior art embodiments.
The term “halogen” refers to radicals of fluorine, chlorine, bromine and iodine.
The term “alkyl” refers to a straight or branched hydrocarbon chain radical, containing solely carbon and hydrogen atoms, having in the range from one up to eight carbon atoms, and which is attached to the rest of the molecule by a single bond, such as illustratively, methyl, ethyl, n-propyl 1-methylethyl (iso-propyl), n-butyl, n-pentyl, and 1,1-dimethylethyl (tert-butyl).
The term “cycloalkyl” denotes a non-aromatic mono or multicyclic ring system having in the range of 3 up to 14 carbon atoms such as cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Examples of multicyclic cycloalkyl groups include decahydronapththyl. Examples of bridged cycloalkyl groups or sprirobicycloalkyl groups include adamantyl norbornyl, and sprio[4.4]nonyl groups.
The term “alkoxy” denotes an alkyl group as defined herein attached via an oxygen linkage to the rest of the molecule. Representative examples of those groups are methoxy, ethoxy, iso-propoxy, n-butoxy, and tert-butoxy.
The term “cycloalkoxy” denotes a cycloalkyl group as defined herein attached via an oxygen linkage to the rest of the molecule. Representative examples of those groups are cyclopropoxy, cyclobutoxy, cyclopentoxy, cyclohexoxy, and cycloheptoxy.
The term “aryl” refers to aromatic radicals having in the range of 6 up to 14 carbon atoms such as phenyl, naphthyl, indanyl, and biphenyl.
The term “heteroaryl” refers to a stable 5- to 13-membered aromatic heterocycle having in the range of from 1 up to 4 heteroatoms from the group consisting of nitrogen, phosphorus, oxygen and sulfur, which ring or ring system can be linked via a carbon atom or a nitrogen atom, if such an atom is present. For purposes of this invention, the heteroaryl ring radical may be a monocyclic, bicyclic or tricyclic ring system. Examples of such heteroaryl radicals are: pyridyl, pyridyl N-oxide, pyrimidyl, pyridazinyl, pyrazinyl, thienyl, furyl, pyrrolyl, pyrazolyl, imidazolyl, thiazolyl, oxazolyl or isoxazolyl, indolicenyl, indolyl, benzo[b]thienyl, benzo[b]furyl, benzothiazolyl, benzothiadiazolyl, indazolyl, quinolyl, isoquinolyl, isoquinolyl, naphthyridinyl, quinazolinyl, oxadiazolyl, benzoxazolyl, tetrazoyl, triazolyl, thiadiazolyl, and benzimidazolyl.
The term “heterocycloalkyl” refers to a stable 3 to 13 membered saturated or partially unsaturated heterocycle having in the range from 1 up to 4 heteroatoms from the group consisting of nitrogen, phosphorus, oxygen and sulfur, which ring or ring system can be linked via a carbon atom or a nitrogen atom, if such an atom is present. For purposes of this invention, the heterocyclic ring radical may be a monocyclic, bicyclic or tricyclic ring system, which may include fused, bridged or spiro ring systems. Examples of such heterocyclyl radicals are: tetrahydropyranyl, aziridyl, azepanyl, tetrahydrofuryl, pyrrolidinyl, pyrrolinyl, piperidinyl, 1,2 dihydropyridinyl, 1,4 dihydropyridinyl, piperazinyl, morpholinyl, thiomorpholinyl, azepinyl, oxazolinyl, thiazolinyl and 1,4 diazepinyl.
The term “alkylamino” refers to an alkyl group as defined herein attached via amino linkage to the rest of the molecule. The term alkylamino further includes dialkyl amino moieties in which two alkyl groups as define herein are attached via amino linkage to the rest of the molecule. Representative examples of those groups are methylamino and dimethylamino.
Where the plural form of the word compounds, salts, polymorphs, hydrates, solvates and the like, is used herein, this is taken to mean also a single compound, salt, polymorph, isomer, hydrate, solvate or the like.
The compounds of this invention may contain one or more asymmetric centers, depending upon the location and nature of the various substituents desired. Asymmetric carbon atoms may be present in the (R) or (S) configuration, resulting in racemic mixtures in the case of a single asymmetric center, and diastereomeric mixtures in the case of multiple asymmetric centers. In certain instances, asymmetry may also be present due to restricted rotation about a given bond, for example, the central bond adjoining two substituted aromatic rings of the specified compounds. Substituents on a ring may also be present in either cis or trans form. It is intended that all such configurations (including enantiomers and diastereomers), are included within the scope of the present invention. Preferred compounds are those which produce the more desirable biological activity. Separated, pure or partially purified isomers and stereoisomers or racemic or diastereomeric mixtures of the compounds of this invention are also included within the scope of the present invention. The purification and the separation of such materials can be accomplished by standard techniques known in the art.
The optical isomers can be obtained by resolution of the racemic mixtures according to conventional processes, for example, by the formation of diastereoisomeric salts using an optically active acid or base or formation of covalent diastereomers. Examples of appropriate acids are tartaric, diacetyltartaric, ditoluoyltartaric and camphorsulfonic acid. Mixtures of diastereoisomers can be separated into their individual diastereomers on the basis of their physical and/or chemical differences by methods known in the art, for example, by chromatography or fractional crystallization. The optically active bases or acids are then liberated from the separated diastereomeric salts. A different process for separation of optical isomers involves the use of chiral chromatography (e.g., chiral HPLC columns), with or without conventional derivitization, optimally chosen to maximize the separation of the enantiomers. Suitable chiral HPLC columns are manufactured by Diacel, e.g., Chiracel OD and Chiracel OJ among many others, all routinely selectable. Enzymatic separations, with or without derivitization, are also useful. The optically active compounds of this invention can likewise be obtained by chiral syntheses utilizing optically active starting materials.
The present invention also relates to useful forms of the compounds as disclosed herein, such as pharmaceutically acceptable salts, co-precipitates, metabolites, hydrates, solvates and prodrugs of all the compounds of examples. The term “pharmaceutically acceptable salt” refers to a relatively non-toxic, inorganic or organic acid addition salt of a compound of the present invention. For example, see S. M. Berge, et al. “Pharmaceutical Salts,” J. Phann. Sci. 1977, 66, 1-19. Pharmaceutically acceptable salts include those obtained by reacting the main compound, functioning as a base, with an inorganic or organic acid to form a salt, for example, salts of hydrochloric acid, sulfuric acid, phosphoric acid, methane sulfonic acid, camphor sulfonic acid, oxalic acid, maleic acid, succinic acid and citric acid.
Pharmaceutically acceptable salts also include those in which a compound of the invention functions as an acid and is reacted with an appropriate base to form, e.g., sodium, potassium, calcium, magnesium, ammonium, and chorine salts. Those skilled in the art will further recognize that acid addition salts of the claimed compounds may be prepared by reaction of a compound of the invention the appropriate inorganic or organic acid via any of a number of known methods. Alternatively, alkali and alkaline earth metal salts of acidic compounds of the invention are prepared by reacting the compounds of the invention with the appropriate base via a variety of known methods.
Representative salts of a compound of the invention include the conventional non-toxic salts and the quaternary ammonium salts which are formed, for example, from inorganic or organic acids or bases by means well known in the art. For example, such acid addition salts include acetate, adipate, alginate, ascorbate, aspartate, benzoate, benzenesulfonate, bisulfate, butyrate, citrate, camphorate, camphorsulfonate, cinnamate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, fumarate, glucoheptanoate, glycerophosphate, hemisulfate, heptanoate, hexanoate, hydrochloride, hydrobromide, hydroiodide, 2-hydroxyethanesulfonate, itaconate, lactate, maleate, mandelate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oxalate, pamoate, pectinate, persulfate, 3-phenylpropionate, picrate, pivalate, propionate, succinate, sulfonate, tartrate, thiocyanate, tosylate, and undecanoate.
Base salts include alkali metal salts such as potassium and sodium salts, alkaline earth metal salts such as calcium and magnesium salts, and ammonium salts with organic bases such as dicyclohexylamine and N-methyl-D-glucamine. Additionally, basic nitrogen containing groups may be quaternized with such agents as lower alkyl halides such as methyl, ethyl, propyl, and butyl chlorides, bromides and iodides; diallcyl sulfates like dimethyl, diethyl, and dibutyl sulfate; and diamyl sulfates, long chain halides such as decyl, lauryl, myristyl and stearyl chlorides, bromides and iodides, aralkyl halides like benzyl and phenethyl bromides and others.
A solvate for the purpose of this invention is a complex of a solvent and a compound of the invention in the solid state. Exemplary solvates would include, but are not limited to, complexes of a compound of the invention with ethanol or methanol. Hydrates are a specific form of solvate wherein the solvent is water.
The term “subject” refers to animals such as mammals, including, but not limited to, primates (e.g., humans), cows, sheep, goats, horses, dogs, cats, rabbits, rats, mice and the like. In certain embodiments, the subject is a human.
It is also to be understood that the terminology used herein is for purposes of describing particular embodiments only, and is not intended to be limiting. As used in the specification and the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the context clearly indicates otherwise. Thus, for example, reference to “a peptide” includes multiple peptides, reference to “a spacer” includes two or more spacers.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. In case of conflict, the present application, including definitions will control. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference.

Compounds

As set forth above, the invention provides compounds which selectively bind to the survival protein MCL-1 with high affinity and selectivity.
Table 1 (including Subtables Table 1-A through Table 1-P) lists of representative compounds and subclasses identified as selective or preferential MCL-1 binders based upon a small molecule competitive binding assay using FITC-MCL-1 SAHB/MCL-1ΔNΔC and FITC-BAD BH3/BCL-X_LΔC interaction pairs. FIGS. 4C and 4D tabulates select derivatives of Class A and Class J compounds that exhibit differential MCL-1 targeting activity based on chemical variation of discrete R groups.
Certain compounds of Table 1 describe certain known bioactive compounds. These compounds are particularly useful in targeting MCL-1 and may be useful in the treatment of diseases as described herein. Thus, in certain aspects, the compounds of Formula A-L may exclude certain compounds of Table 1.
The compounds of the invention may contain one or more asymmetric centers and thus occur as racemates and racemic mixtures, single enantiomers, individual diastereomers and diastereomeric mixtures. All such isomeric forms of these compounds are expressly included in the invention. The compounds of this invention may also be represented in multiple tautomeric forms, in such instances, the invention expressly includes all tautomeric forms of the compounds described herein. All such isomeric forms of such compounds are expressly included in the invention. All crystal forms of the compounds described herein are expressly included in the invention.
Naturally occurring or synthetic isomers can be separated in several ways known in the art. Methods for separating a racemic mixture of two enantiomers include chromatography using a chiral stationary phase (see, e.g., “Chiral Liquid Chromatography,” W. J. Lough, Ed. Chapman and Hall, New York (1989)). Enantiomers can also be separated by classical resolution techniques. For example, formation of diastereomeric salts and fractional crystallization can be used to separate enantiomers. For the separation of enantiomers of carboxylic acids, the diastereomeric salts can be formed by addition of enantiomerically pure chiral bases such as brucine, quinine, ephedrine, strychnine, and the like. Alternatively, diastereomeric esters can be formed with enantiomerically pure chiral alcohols such as menthol, followed by separation of the diastereomeric esters and hydrolysis to yield the free, enantiomerically enriched carboxylic acid. For separation of the optical isomers of amino compounds, addition of chiral carboxylic or sulfonic acids, such as camphorsulfonic acid, tartaric acid, mandelic acid, or lactic acid can result in formation of the diastereomeric salts.
Methods of obtaining a compound of the invention include purchasing, synthesizing or otherwise acquiring the compound. Synthesizing a compound of the invention is within the means of chemists of ordinary skill in the art. Methods for optimizing reaction conditions, if necessary minimizing competing by-products, are known in the art. The methods may also additionally include steps, either before or after the steps described specifically herein, to add or remove suitable protecting groups in order to ultimately allow synthesis of the compounds herein. In addition, various synthetic steps may be performed in an alternate sequence or order to give the desired compounds. Synthetic chemistry transformations and protecting group methodologies (protection and deprotection) useful in synthesizing the applicable compounds are known in the art and include, for example, those described in R. Larock, Comprehensive Organic Transformations, VCH Publishers (1989); T. W. Greene and P. G. M. Wuts, Protective Groups in Organic Synthesis, 3rd Ed., John Wiley and Sons (1999); L. Fieser and M. Fieser, Fieser and Fieser's Reagents for Organic Synthesis, John Wiley and Sons (1994); and L. Paquette, ed., Encyclopedia of Reagents for Organic Synthesis, John Wiley and Sons (1995) and subsequent editions thereof
Methods of Treatment
In one aspect, the invention encompasses a method of modulating MCL-1 in a cell comprising contacting a cell with one or more compounds of the invention. Such modulation is useful in the modulation of programmed cell death or apoptosis, autophagic cell death; necrotic cell death; cell metabolism; cell division; cell differentiation; cell migration; cell engraftinent; tissue repair; RNA transcription and processing; or protein multimerization or dissociation.
As used herein, the term “modulation” refers to a change in activity as a direct or indirect response to the presence of at least one compound of the invention described herein, relative to the activity in the absence of the compound. The change may be an increase in activity or a decrease in activity, and may be due to the direct interaction of the compound with MCL-1, or due to the interaction of the compound with one or more other factors that in turn interact with MCL-1 or affect MCL-1 activity. In certain embodiments, the modulation may be the result of a covalent bond between the compound with MCL-1. In certain embodiments, the modulation may be the result of a non-covalent bond between the compound with MCL-1. In certain embodiments, the modulation may be the result of a covalent bond between the compound with the established BH3 binding site of MCL-1 or with a residue of MCL-1 not associated with the established BH3 binding site of MCL-1. In certain embodiments, the modulation may be the result of a non-covalent bond between the compound with the established BH3 binding site of MCL-1 or with a residue of MCL-1 not associated with the established BH3 binding site of MCL-1. In still other embodiments, the modulation may be the result of a covalent bond between the compound with the C286 reside of MCL-1. In certain embodiments, the modulation may be the result of a non-covalent bond between the compound in the region of the C286 residue of MCL-1.
In one aspect, the invention encompasses a method of treating a hyperproliferative disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
As used herein the term “hyperproliferative disorder” refers to a disorder associated with an irregular or an abnormally high rate of cell division (which results in a rapid proliferation of the cells) or a blockade in the natural cell death pathway resulting in the accumulation of cells, or a combination thereof. Hyperproliferative disorders include but are not limited, e.g., psoriasis, keloids, and other hyperplasias affecting the skin, benign prostate hyperplasia (BPH), solid and liquid tumors, such as cancers of the breast, respiratory tract, brain, reproductive organs, digestive tract, urinary tract, eye, liver, skin, head and neck, thyroid, parathyroid and their distant metastases, lymphomas, sarcomas, and leukemias.
Still another aspect of the invention encompasses a method of treating a cell cycle regulation disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
As used herein, the term “cell cycle regulation disorder” relates to a disorder of the cell cycle regulation mechanisms, observed in many malignant tumors, are directly related to uncontrolled proliferation of cancer cells. Cell cycle regulation disorders can be the result of the degradation of the regulation of one or more stages of cell growth, G₁, S, G₂, and M phases of the growth cycle and may include the degradation of one or more cell cycle regulators including, but not limited to, p27Kip1, cdk2, cdk4, cdk6, chk1, cdc25, cyclin B, cyclin H, cyclin D, and cyclin E.
Examples of breast cancer include, but are not limited to invasive ductal carcinoma, invasive lobular carcinoma, ductal carcinoma in situ, and lobular carcinoma in situ.
Examples of cancers of the respiratory tract include, but are not limited to small-cell and non-small-cell lung carcinoma, as well as bronchial adenoma and pleuropulmonary blastoma.
Examples of brain cancers include, but are not limited to brain stem and hypophtalmic glioma, cerebellar and cerebral astrocytoma, medulloblastoma, ependymoma, as well as neuroectodermal and pineal tumor.
Tumors of the male reproductive organs include, but are not limited to prostate and testicular cancer. Tumors of the female reproductive organs include, but are not limited to endometrial, cervical, ovarian, vaginal, and vulvar cancer, as well as sarcoma of the uterus.
Tumors of the digestive tract include, but are not limited to anal, colon, colorectal, esophageal, gallbladder, gastric, pancreatic, rectal, small-intestine, and salivary gland cancers.
Tumors of the urinary tract include, but are not limited to bladder, penile, kidney, renal pelvis, ureter, urethral and human papillary renal cancers.
Eye cancers include, but are not limited to intraocular melanoma and retinoblastoma.
Examples of liver cancers include, but are not limited to hepatocellular carcinoma (liver cell carcinomas with or without fibrolamellar variant), cholangiocarcinoma (intrahepatic bile duct carcinoma), and mixed hepatocellular cholangiocarcinoma.
Skin cancers include, but are not limited to squamous cell carcinoma, Kaposi's sarcoma, malignant melanoma, Merkel cell skin cancer, and non-melanoma skin cancer.
Head-and-neck cancers include, but are not limited to laryngeal, hypopharyngeal, nasopharyngeal, oropharyngeal cancer, lip and oral cavity cancer and squamous cell. Lymphomas include, but are not limited to AIDS-related lymphoma, non-Hodgkin's lymphoma, cutaneous T-cell lymphoma, Burkitt lymphoma, Hodgkin's disease, and lymphoma of the central nervous system.
Sarcomas include, but are not limited to sarcoma of the soft tissue, osteosarcoma, malignant fibrous histiocytoma, lymphosarcoma, and rhabdomyosarcoma.
Leukemias include, but are not limited to acute myeloid leukemia, acute lymphoblastic leukemia, chronic lymphocytic leukemia, chronic myelogenous leukemia, and hairy cell leukemia.
In one aspect, the invention encompasses a method of treating angiogenesis in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
As used herein the term “angiogenesis” refers to a disorder associated with excessive and/or abnormal angiogenesis.
Inappropriate and ectopic expression of angiogenesis can be deleterious to an organism. A number of pathological conditions are associated with the growth of extraneous blood vessels. These include, e.g., diabetic retinopathy, ischemic retinal-vein occlusion, and retinopathy of prematurity (Aiello et al. New Engl. J. Med. 1994, 331, 1480; Peer et al. Lab. Invest. 1995, 72, 638), age-related macular degeneration (AMD; see, Lopez et al. Invest. Opththalmol. Vis. Sci. 1996, 37, 855), neovascular glaucoma, psoriasis, retrolental fibroplasias, angiofibroma, inflammation, rheumatoid arthritis (RA), restenosis, in-stent restenosis, vascular graft restenosis, etc. In addition, the increased blood supply associated with cancerous and neoplastic tissue, encourages growth, leading to rapid tumor enlargement and metastasis. Moreover, the growth of new blood and lymph vessels in a tumor provides an escape route for renegade cells, encouraging metastasis and the consequence spread of the cancer. Thus, compounds of the present invention can be utilized to treat and/or prevent any of the aforementioned angiogenesis disorders, e.g., by inhibiting and/or reducing blood vessel formation; by inhibiting, blocking, reducing, decreasing, etc. endothelial cell proliferation or other types involved in angiogenesis, as well as causing cell death or apoptosis of such cell types.
Another aspect of the invention encompasses a method of treating an infectious disease by blocking pathogen or infected cell survival in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Examples of infectious diseases include, but are not limited to, AIDS, Alveolar Hydatid Disease (AHD, Echinococcosis), Amebiasis (Entamoeba histolytica Infection), Angiostrongylus Infection, Anisakiasis, Anthrax, Babesiosis (Babesia Infection), Balantidium Infection (Balantidiasis), Baylisascaris Infection (Raccoon Roundworm), Bilharzia (Schistosomiasis), Blastocystis hominis Infection (Blastomycosis), Boreliosis, Botulism, Brainerd Diarrhea, Brucellosis, BSE (Bovine Spongiform Encephalopathy), Candidiasis, Capillariasis (Capillaria Infection), CFS (Chronic Fatigue Syndrome), Chagas Disease (American Trypanosomiasis), Chickenpox (Varicella-Zoster virus), Chlamydia pneumoniae Infection, Cholera, Chronic Fatigue Syndrome, CJD (Creutzfeldt-Jakob Disease), Clonorchiasis (Clonorchis Infection), CLM (Cutaneous Larva Migrans, Hookworm Infection), Coccidioidomycosis, Conjunctivitis, Coxsackievirus A16 (Hand, Foot and Mouth Disease), Cryptococcosis, Cryptosporidium Infection (Cryptosporidiosis), Culex mosquito (Vector of West Nile Virus), Cutaneous Larva Migrans (CLM), Cyclosporiasis (Cyclospora Infection), Cysticercosis (Neurocysticercosis), Cytomegalovirus Infection, Dengue/Dengue Fever, Dipylidium Infection (Dog and Cat Flea Tapeworm), Ebola Virus Hemorrhagic Fever, Echinococcosis (Alveolar Hydatid Disease), Encephalitis, Entamoeba coli Infection, Entamoeba dispar Infection, Entamoeba hartmanni Infection, Entamoeba histolytica Infection (Amebiasis), Entamoeba polecki Infection, Enterobiasis (Pinworm Infection), Enterovirus Infection (Non-Polio), Epstein-Barr Virus Infection, Escherichia coli Infection, Foodborne Infection, Foot and mouth Disease, Fungal Dermatitis, Gastroenteritis, Group A streptococcal Disease, Group B streptococcal Disease, Hansen's Disease (Leprosy), Hantavirus Pulmonary Syndrome, Head Lice Infestation (Pediculosis), Heliobacter pylori Infection, Hematologic Disease, Hendra Virus Infection, Hepatitis (HCV, HBV), Herpes Zoster (Shingles), HIV Infection, Human Ehrlichiosis, Human Parainfluenza Virus Infection, Influenza, Isosporiasis (Isospora Infection), Lassa Fever, Leishmaniasis, Kala-azar (Kala-azar, Leishmania Infection), Lice (Body lice, Head lice, Pubic lice), Lyme Disease, Malaria, Marburg Hemorrhagic Fever, Measles, Meningitis, Mosquito-borne Diseases, Mycobacterium avium Complex (MAC) Infection, Naegleria Infection, Nosocomial Infections, Nonpathogenic Intestinal Amebae Infection, Onchocerciasis (River Blindness), Opisthorciasis (Opisthorcis Infection), Parvovirus Infection, Plague, PCP (Pneumocystis carinii Pneumonia), Polio, Q Fever, Rabies, Respiratory Syncytial Virus (RSV) Infection, Rheumatic Fever, Rift Valley Fever, River Blindness (Onchocerciasis), Rotavirus Infection, Roundworms Infection, Salmonellosis, Salmonella Enteritidis, Scabies, Shigellosis, Shingles, Sleeping Sickness, Smallpox, Streptococcal Infection, Tapeworm Infection (Taenia Infection), Tetanus, Toxic Shock Syndrome, Tuberculosis, Ulcers (Peptic Ulcer Disease), Valley Fever, Vibrio parahaemolyticus Infection, Vibrio vulnificus Infection, Viral Hemorrhagic Fever, Warts, Waterborne infectious Diseases, West Nile Virus Infection (West Nile Encephalitis), Whooping Cough, Yellow Fever, tuberculosis, leprosy, mycobacteria-induced meningitis, Chagas disease, effects of Shiga-like toxin resulting from Staphylococcus infection, meningococcal infection, and infections from Borrelia burgdorferi or Treponema pallidum.
Yet another aspect of the invention encompasses a method of treating an autophagy regulation disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
As used herein, the term “autophagy regulation disorder” relates to a dissorder of the autophagy system of a cell i.e. the self-digestion by a cell through the action of enzymes originating within the same cell including, but not limited to, chaperone-mediated autophagy, macroautophagy, microautophagy. Disorders of autophagy regulation include but are not limited to, Danon disease X-linked myopathy with excessive autophagy, Infantile autophagic vacuolar myopathy, Childhood autophagic vacuolar myopathy, Adult-onset autophagic vacuolar myopathy with multiorgan involvement, LGMD 1A, Toxic myopathy, Inflammatory myopathies, Hypokalemic myopathy, Acid maltase deficiency, Inflammatory bowel disease associations, Autophagy 16-like 1 (ATG16L1), LRG47, and autophagy-mediated survival of cancer cells or cancer stem cells to escape chemotherapy or radiation treatments.
Still yet another aspect of the invention provides a method of treating an autoimmune disorder in a mammal comprising administering to a mammal in need thereof, a therapeutically effective amount of one or more compounds of the invention.
Examples of autoimmune disorders include, but are not limited to, allergic bronchopulmonary aspergillosis; autoimmune hemolytic anemia; acanthosis nigricans; allergic contact dermatitis; Addison's disease; atopic dermatitis; alopecia greata; alopecia universalis; amyloidosis; anaphylactoid purpura; anaphylactoid reaction; aplastic anemia; angioedema, hereditary; angioedema, idiopathic; ankylosing spondylitis; arteritis, cranial; arteritis, giant cell; arteritis, Takayasu's; arteritis, temporal; asthma; a-telangiectasia; autoimmune oophoritis; autoimmune orchitis; autoimmune polyendocrine failure; Behcet's disease; Berger's disease; Buerger's disease; bullous pemphigus; candidiasis, chronic mucocutaneous; Caplan's syndrome; post-myocardial infarction syndrome; post-pericardiotomy syndrome; carditis; celiac sprue; Chagas's disease; Chediak-Higashi syndrome; Churg-Strauss disease; Cogan's syndrome; cold agglutinin disease; CREST syndrome; Crohn's disease; cryoglobulinemia; cryptogenic fibrosing alveolitis; dermatitis herpetifomis; dermatomyositis; diabetes mellitus; Diamond-Blackfan syndrome; DiGeorge syndrome; discoid lupus erythematosus; eosinophilic fascitis; episcleritis; drythema elevatum diutinum; erythema marginatum; erythema multiforme; erythema nodosum; familial Mediterranean fever; Felty's syndrome; fibrosis pulmonary; glomerulonephritis, anaphylactoid; glomerulonephritis, autoimmune; glomerulonephritis, post-streptococcal; glomerulonephritis, post-transplantation; glomerulopathy, membranous; Goodpasture's syndrome; graft-vs.-host disease; granulocytopenia, immune-mediated; granuloma annulare; granulomatosis, allergic; granulomatous myositis; Grave's disease; Hashimoto's thyroiditis; hemolytic disease of the newborn; hemochromatosis, idiopathic; Henoch-Schoenlein purpura; hepatitis, chronic active and chronic progressive; histiocytosis X; hypereosinophilic syndrome; idiopathic thrombocytopenic purpura; Job's syndrome; juvenile dermatomyositis; juvenile rheumatoid arthritis juvenile chronic arthritis); Kawasaki's disease; keratitis; keratoconjunctivitis sicca; Landry-Guillain-Barre-Strohl syndrome; leprosy, lepromatous; Loeffler's syndrome; Lyell's syndrome; Lyme disease; lymphomatoid granulomatosis; mastocytosis, systemic; mixed connective tissue disease; mononeuritis multiplex; Muckle-Wells syndrome; mucocutaneous lymph node syndrome; mucocutaneous lymph node syndrome; multicentric reticulohistiocytosis; multiple sclerosis; myasthenia gravis; mycosis fungoides; necrotizing vasculitis, systemic; nephrotic syndrome; overlap syndrome; panniculitis; paroxysmal cold hemoglobinuria; paroxysmal nocturnal hemoglobinuria; pemphigoid; pemphigus; pemphigus erythematosus; pemphigus foliaceus; pemphigus vulgaris; pigeon breeder's disease; pneumonitis, hypersensitivity; polyarteritis nodosa; polymyalgia rheumatica; polymyositis; polyneuritis, idiopathic; Portuguese familial polyneuropathies; pre-eclampsia/eclampsia; primary biliary cirrhosis; progressive systemic sclerosis (scleroderma); psoriasis; psoriatic arthritis; pulmonary alveolar proteinosis; pulmonary fibrosis, Raynaud's phenomenon/syndrome; Reidel's thyroiditis; Reiter's syndrome, relapsing polychrondritis; rheumatic fever; rheumatoid arthritis; sarcoidosis; scleritis; sclerosing cholangitis; serum sickness; Sezary syndrome; Sjogren's syndrome; Stevens-Johnson syndrome; Still's disease; subacute sclerosing panencephalitis; sympathetic ophthalmia; systemic lupus erythematosus; transplant rejection; ulcerative colitis; undifferentiated connective tissue disease; urticaria, chronic; urticaria, cold; uveitis; vitiligo; Weber-Christian disease; Wegener's granulomatosis; and Wiskott-Aldrich syndrome.
In another aspect, the invention provides a method of enhancing cellular engraftment in a subject comprising administering to a subject in need thereof of a therapeutically effective amount of one or more compounds of the invention.
As used herein the phrase “enhancing cellular engraftment” refers to an improvement in efficiency, quality or rapidity of cell transplantation which may result from improved homing to the target tissue, improved adhesion, reduced rejection and the like. Methods for assessing cell engraftment potential include, for example, cell migration and other in vitro techniques, and histological, immunological and/or radiological assessment of tissues and organs from actual in-vivo transplantation. In certain aspects, the term “enhancing cellular engraftment” also includes, but is not limited to, the treatment of a disorder in which the subject is treated with cells, such as in the context of bone marrow transplantation, stem cell replacement, and skin engraftment.
In another aspect, the invention provides a method of enhancing wound repair in a subject comprising administering to a subject in need thereof of a therapeutically effective amount of one or more compounds of the invention.
As used herein the term, “enhancing wound repair” includes, but is not limited to, the formation of granulation tissue; of wound contraction; and/or the induction of epithelialization (i.e., the generation of new cells in the epithelium). Wound repair is conveniently measured by decreasing wound area. In certain aspects, the term “enhancing wound repair” also includes, but is not limited to, the treatment a disorder in which the subject is being treated for tissue damage, either internal or external, such that the goal is to restore organ or tissue integrity.
In another aspect, the invention provides a method of treating an inflammatory condition in a subject comprising administering to a subject in need thereof an effective amount of a composition comprising a compound of the invention or a pharmaceutically acceptable salt thereof.
As used herein, the term “inflammatory condition” refers to a condition or disorder associated with one or more aberrant physiological processes or other physiological responses (such as responses to an injurious or noxious stimulus) which result in a pathophysiological state of inflammation. An inflammatory condition may be either an acute or chronic inflammatory condition, which can result from infections or non-infectious causes. Various infectious causes include meningitis, encephalitis, uveitis, colitis, tuberculosis, dermatitis, and adult respiratory distress syndrome. Non-infectious causes include trauma (burns, cuts, contusions, crush injuries), autoimmune diseases, and organ rejection episodes. Thus, in specific aspects, an inflammatory condition results from a condition selected from the group that includes: atherosclerosis (arteriosclerosis); autoimmune conditions, such as multiple sclerosis, systemic lupus erythematosus, polymyalgia rheumatica (PMR), gouty arthritis, degenerative arthritis, tendonitis, bursitis, psoriasis, fibrosis, arthrosteitis, rheumatoid arthritis and other forms of inflammatory arthritis, Sjogren's Syndrome, progressive systemic sclerosis (scleroderma), ankylosing spondylitis, polymyositis, dermatomyositis, pemphigus, pemphigoid, Type I diabetes mellitus, myasthenia gravis, Hashimoto's thyroditis, Graves' disease, Goodpasture's disease, mixed connective tissue disease, sclerosing cholangitis, inflammatory bowel disease including Crohn's Disease (regional enteritis) and ulcerative colitis, pernicious anemia, inflammatory dermatoses; usual interstitial pneumonitis (UV), asbestosis, silicosis, bronchiectasis, berylliosis, talcosis, all forms of pneumoconiosis, sarcoidosis (in the lung and in any other organ), desquamative interstitial pneumonia, lymphoid interstitial pneumonia, giant cell interstitial pneumonia, cellular interstitial pneumonia, extrinsic allergic alveolitis, Wegener's granulomatosis and related forms of angiitis (temporal arteritis and polyarteritis nodosa); sepsis; inflammatory dermatoses not presumed to be autoimmune; chronic active hepatitis; delayed-type hypersensitivity reactions (e.g., poison ivy dermatitis); pneumonia or other respiratory tract inflammation due to any cause; Adult Respiratory Distress Syndrome (ARDS) from any etiology; encephalitis with inflammatory edema; immediate hypersensitivity reactions including, but not limited to, asthma, hayfever, cutaneous allergies, acute anaphylaxis; diseases involving acute deposition of immune complexes, including, but not limited to, rheumatic fever, acute and/or chronic glomerulonephritis due to any etiology, including specifically post-infectious (e.g., post-Streptococcal) glomerulonephritis, acute exacerbations of Systemic Lupus Erythematosus; pyelonephritis; cellulitis; cystitis; acute and/or chronic cholecystitis; and conditions producing transient ischemia anywhere along the gastrointestinal tract, bladder, heart, or other organ, especially those prone to rupture; sequelae of organ transplantation or tissue allograft, including allograft rejection in the acute time period following allogeneic organ or tissue transplantation and chronic host-versus-graft rejection. The term “inflammatory condition” also includes appendicitis, arteritis, blepharitis, bronchiolitis, bronchitis, cervicitis, cholangitis, chorioamnionitis, conjunctivitis, dacryoadenitis, dermatomyositis, endocarditis, endometritis, enteritis, enterocolitis, epicondylitis, epididymitis, fasciitis, fibrositis, gastritis, gastroenteritis, gingivitis, ileitis, iritis, laryngitis, myelitis, myocarditis, nephritis, omphalitis, oophoritis, orchitis, osteitis, otitis, pancreatitis, parotitis, pericarditis, pharyngitis, pleuritis, phlebitis, pneumonitis, proctitis, prostatitis, rhinitis, salpingitis, sinusitis, stomatitis, synovitis, tonsillitis, uveitis, vaginitis, vasculitis, vulvitis, and vulvovaginitis, angitis, chronic bronchitis, osteomylitis, optic neuritis, temporal arteritis, transverse myelitis, necrotizing fascilitis, hepatitis, and necrotizing enterocolitis.
In a specific aspect, the invention encompasses a method of targeting MCL-1 in a cell comprising contacting a, cell with one or more compounds selected from gossypol, celastrol, manoalide, u73122, bithionol and hexachlorophene. Such targeting may useful in the modulation of programmed cell death or apoptosis, autophagic cell death; necrotic cell death; cell metabolism; cell division; cell differentiation; RNA transcription and processing; or protein multimerization or dissociation.
As used herein, the term “targeting” refers to the direct interaction of the compound with MCL-1, or to the interaction of the compound with one or more other factors that in turn interact with MCL-1 or affect MCL-1 activity.
Administration
In certain embodiments, a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof is administered to the subject in a pharmaceutically-acceptable formulation. In certain embodiments, a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof or an a compound of the invention pharmaceutical composition is suitable for topical, intravenous, parental, or oral administration. The methods of the invention further include administering to a subject a therapeutically effective amount of a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof.
The phrase “pharmaceutically acceptable” refers to a compound of the invention, compositions containing a compound of the invention, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
The phrase “pharmaceutically-acceptable carrier” includes pharmaceutically-acceptable material, composition or vehicle, involved in carrying or transporting the subject chemical from one organ, or portion of the body, to another organ, or portion of the body. Each carrier must be “acceptable” in the sense of being compatible with the other ingredients of the formulation and not injurious to the patient.
Methods of preparing these compositions include the step of bringing into association a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof with the carrier and, optionally, one or more accessory ingredients. These compositions may also contain adjuvants such as preservatives, wetting agents, emulsifying agents and dispersing agents.
Regardless of the route of administration selected, a compound of the invention, which may be used in a suitable salt, solvate, or hydrate form, and/or the pharmaceutical compositions of a compound of the invention, are formulated into pharmaceutically acceptable dosage forms by conventional methods known to those of skill in the art.
Formulations are provided to a subject in an effective amount. The term “effective amount” includes an amount effective, at dosages and for periods of time necessary, to achieve the desired result. An effective amount of a compound of the invention may vary according to factors such as the disease state, age, and weight of the subject, and the ability of the compound to elicit a desired response in the subject. Dosage regimens may be adjusted to provide the optimum therapeutic response.
The effective amount is generally determined by the physician on a case-by-case basis and is within the skill of one in the art. As a rule, the dosage for in vivo therapeutics or diagnostics will vary. Several factors are typically taken into account when determining an appropriate dosage. These factors include age, sex and weight of the patient, the condition being treated, and the severity of the condition. In addition, an effective amount is preferably selected to minimize adverse side effects. For example, an effective amount of a compound of the invention is preferably selected to treat or prevent a disorder as disclosed herein, while minimizing side effects such as hypotension.
Suitable dosages and formulations of a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof can be empirically determined by the administering physician. Standard texts, such as Remington: The Science and Practice of Pharmacy, 17th edition, Mack Publishing Company, and the Physician's Desk Reference, each of which are incorporated herein by reference, can be consulted to prepare suitable compositions and doses for administration. A determination of the appropriate dosage is within the skill of one in the art given the parameters for use described herein.
Standard texts, such as Remington: The Science and Practice of Pharmacy, 17th edition, Mack Publishing Company, incorporated herein by reference, can be consulted to prepare suitable compositions and formulations for administration, without undue experimentation. Suitable dosages can also be based upon the text and documents cited herein. A determination of the appropriate dosages is within the skill of one in the art given the parameters herein.
In terms of treatment, an effective amount is an amount that is sufficient to palliate, ameliorate, stabilize, reverse or slow the progression of an inflammatory condition or other disorder as disclosed herein, or the symptoms thereof. A therapeutically effective amount can be provided in one or a series of administrations. In terms of an adjuvant, an effective amount is one sufficient to enhance the anti-inflammatory or immune response to the anti-inflammatory or immunogen. The effective amount is generally determined by the physician on a case-by-case basis and is within the skill of one in the art.
As a rule, the dosage for in vivo therapeutics or diagnostics will vary. Several factors are typically taken into account when determining an appropriate dosage. These factors include age, sex and weight of the patient, the condition being treated, the severity of the condition and the method of administration.
The dosage of a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof can vary from about 0.01 mg to about 1,000 mg per day; about 0.1 mg to about 250 mg per day; about 0.5 mg to about 100 mg per day; or about 1 to about 5 mg per day. Ascertaining dosage ranges is well within the skill of one in the art. The dosage of a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof can range from about 0.001 to 25 mg/kg of body weight. Such dosages may vary, for example, depending on whether multiple administrations are given, tissue type and route of administration, the condition of the individual, the desired objective and other factors known to those of skill in the art. Administrations can be conducted infrequently, or on a regular weekly basis until a desired, measurable parameter is detected, such as diminution of disease symptoms. Administration can then be diminished, such as to a biweekly or monthly basis, as appropriate.
A therapeutically effective amount can be administered in one or more doses. The term “administration” or “administering” includes routes of introducing the compound(s) to a subject to perform their intended function. Examples of routes of administration which can be used include injection (subcutaneous, intravenous, parenterally, intraperitoneally, intrathecal), oral, inhalation, rectal and transdermal.
The phrases “parenteral administration” and “administered parenterally” as used herein means modes of administration other than enteral and topical administration, usually by injection, and includes, without limitation, intravenous, intramuscular, intraarterial, intrathecal, intracapsular, intraorbital, intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous, subcuticular, intraarticular, subcapsular, subarachnoid, intraspinal and intrasternal injection and infusion.
The phrases “systemic administration,” “administered systemically”, “peripheral administration” and “administered peripherally” as used herein mean the administration of a compound(s), drug or other material, such that it enters the patient's system and, thus, is subject to metabolism and other like processes, for example, subcutaneous administration.
Such dosages may vary, for example, depending on whether multiple administrations are given, tissue type and route of administration, the condition of the individual, the desired objective and other factors known to those of skill in the art.
Available routes of administration include subcutaneous, intramuscular, intraperitoneal, intradermal, oral, intranasal, intrapulmonary (i.e., by aerosol), intravenously, intramuscularly, subcutaneously, intracavity, intrathecally or transdermally, alone or in combination with other pharmaceutical agents.
A cell can be contacted with a composition including a compound of the invention, in certain embodiments in vivo or, in certain embodiments, in vitro. Contacting a cell in vivo can include administration of the composition to a subject, or to a tissue, such that a cell is contacted with a compound of the invention. Contacting a cell in vitro can include, e.g., contacting the cell with a compound of the invention, or a composition consisting essentially of a compound of the invention, directly or by addition of irinadalone or the composition to a growth medium for the cell.

Additional/Secondary Therapeutic Agents

The compounds and compositions of the invention can be administered with one or more additional therapeutic agents either separately or in the same formulation as a compound of the invention.
In certain embodiments the compounds and compositions of the invention are useful in sensitizing a cell or a subject to one or more secondary therapeutic agents. In such embodiments, the invention provides a method for sensitizing a cell to a secondary therapeutic agent comprising administering to said cell a sensitizing amount of one or more compound of the invention. A sensitizing amount may be any amount capable of generating a greater response by the cell to the secondary therapeutic agent as compared to the response by the cell without a compound or composition of the invention. In certain embodiments a sensitizing amount is a therapeutically effective amount. In other embodiments, a sensitizing amount is less than a therapeutically effective amount.
The compounds and compositions of the invention can be administered with one or more additional therapeutic agents either separately or in the same formulation as a compound of the invention.
Additional Therapeutic agents include, but are not limited to antacids, antibiotics, antiemetic agents, antidepressants, and antifungal agents, anti-inflammatory agents, antiviral agents, anticancer agents, immunomodulatory agents, β-interferons, hormones or cytokines.
Additional Therapeutic agents further include, but are not limited to death receptor stimulants (e.g. TRAIL), HDAC inhibitor (e.g. SAHA), proteasome inhibitor (e.g. Bortezomib), BCL-2 family inhibitor (e.g. ABT-737, ABT-263, obatoclax), kinase inhibitor (e.g. Gleevac, Raf inhibitor), mitotic inhibitors (e.g. Taxol), nucleoside analogs (e.g. Gemcitabine), and anti-cancer monoclonal antibodies (e.g. cetuximab), corticosteroids (e.g. dexamethasone), DNA-damaging agents (e.g. cisplatin), antimetabolites (e.g. methotrexate).
The compounds of the invention can be formulated in combination with antacids. For example, they can be formulated with aluminum carbonate, aluminum hydroxide, bismuth subsalicylate, calcium carbonate, calcium hydroxide, calcium phosphate, dihydroxyaluminum sodium carbonate, magnesium hydroxide, magnesium oxide, magnesium trisilicate, sodium bicarbonate, simethicone, glycine, or combinations thereof. The compounds of the invention can be formulated in combination with antibiotics.
For example, they can be formulated with a macrolide (e.g., tobramycin), a cephalosporin (e.g., cephalexin, cephradine, cefuroxime, cefprozil, cefaclor, cefixime or cefadroxil), a clarithromycin (e.g., clarithromycin), an erythromycin (e.g., erythromycin), a penicillin (e.g., penicillin V) or a quinolone (e.g., ofloxacin, ciprofloxacin or norfloxacin), aminoglycoside antibiotics (e.g., apramycin, arbekacin, bambermycins, butirosin, dibekacin, neomycin, neomycin, undecylenate, netilmicin, paromomycin, ribostamycin, sisomicin, and spectinomycin), amphenicol antibiotics (e.g., azidamfenicol, chloramphenicol, florfenicol, and thiamphenicol), ansamycin antibiotics (e.g., rifamide and rifampin), carbacephems (e.g., loracarbef), carbapenems (e.g., biapenem and imipenem), cephalosporins (e.g., cefaclor, cefadroxil, cefamandole, cefatrizine, cefazedone, cefozopran, cefpimizole, cefpiramide, and cefpirome), cephamycins (e.g., cefbuperazone, cefinetazole, and cefminox), monobactams (e.g., aztreonam, carumonam, and tigemonam), oxacephems (e.g., flomoxef, and moxalactam), penicillins (e.g., amdinocillin, amdinocillin pivoxil, amoxicillin, bacampicillin, benzylpenicillinic acid, benzylpenicillin sodium, epicillin, fenbenicillin, floxacillin, penamccillin, penethamate hydriodide, penicillin o-benethamine, penicillin 0, penicillin V, penicillin V benzathine, penicillin V hydrabamine, penimepicycline, and phencihicillin potassium), lincosamides (e.g., clindamycin, and lincomycin), amphomycin, bacitracin, capreomycin, colistin, enduracidin, enviomycin, tetracyclines (e.g., apicycline, chlortetracycline, clomocycline, and demeclocycline), 2,4-diaminopyrimidines (e.g., brodimoprim), nitrofurans (e.g., furaltadone, and furazolium chloride), quinolones and analogs thereof (e.g., cinoxacing clinafloxacin, flumequine, and grepagloxacin), sulfonamides (e.g., acetyl sulfamethoxypyrazine, benzylsulfamide, noprylsulfamide, phthalylsulfacetamide, sulfachrysoidine, and sulfacytine), sulfones (e.g., diathymosulfone, glucosulfone sodium, and solasulfone), cycloserine, mupirocin and tuberin.
The compounds of the invention can be formulated in combination with an antiemetic agent. Suitable antiemetic agents include, but are not limited to, metoclopromide, domperidone, prochlorperazine, promethazine, chlorpromazine, trimethobenzamide, ondansetron, granisetron, hydroxyzine, acethylleucine monoethanolamine, alizapride, azasetron, benzquinamide, bietanautine, bromopride, buclizine, clebopride, cyclizine, dimenhydrinate, diphenidol, dolasetron, meclizine, methallatal, metopimazine, nabilone, oxyperndyl, pipamazine, scopolamine, sulpiride, tetrahydrocannabinols, thiethylperazine, thioproperazine, tropisetron, and mixtures thereof.
The compounds of the invention can be formulated or formulated in combination with an antidepressant. Suitable antidepressants include, but are not limited to, binedaline, caroxazone, citalopram, dimethazan, fencamine, indalpine, indeloxazine hydrocholoride, nefopam, nomifensine, oxitriptan, oxypertine, paroxetine, sertraline, thiazesim, trazodone, benmoxine, iproclozide, iproniazid, isocarboxazid, nialamide, octamoxin, phenelzine, cotinine, rolicyprine, rolipram, maprotiline, metralindole, mianserin, mirtazepine, adinazolam, amitriptyline, amitriptylinoxide, amoxapine, butriptyline, clomipramine, demexiptiline, desipramine, dibenzepin, dimetacrine, dothiepin, doxepin, fluacizine, imipramine, imipramine N-oxide, iprindole, lofepramine, melitracen, metapramine, nortriptyline, noxiptilin, opipramol, pizotyline, propizepine, protriptyline, quinupramine, tianeptine, trimipramine, adrafinil, benactyzine, bupropion, butacetin, dioxadrol, duloxetine, etoperidone, febarbamate, femoxetine, fenpentadiol, fluoxetine, fluvoxamine, hematoporphyrin, hypericin, levophacetoperane, medifoxamine, milnacipran, minaprine, moclobemide, nefazodone, oxaflozane, piberaline, prolintane, pyrisuccideanol, ritanserin, roxindole, rubidium chloride, sulpiride, tandospirone, thozalinone, tofenacin, toloxatone, tranylcypromine, L-tryptophan, venlafaxine, viloxazine, and zimeldine.
The compounds of the invention can be formulated in combination with an antifungal agent. Suitable antifungal agents include but are not limited to amphotericin B, itraconazole, ketoconazole, fluconazole, intrathecal, flucytosine, miconazole, butoconazole, clotrimazole, nystatin, terconazole, tioconazole, ciclopirox, econazole, haloprogrin, naftifine, terbinafine, undecylenate, and griseofuldin.
The compounds of the invention can be formulated in combination with an anti-inflammatory agent. Useful anti-inflammatory agents include, but are not limited to, non-steroidal anti-inflammatory drugs such as salicylic acid, acetylsalicylic acid, methyl salicylate, diflunisal, salsalate, olsalazine, sulfasalazine, acetaminophen, indomethacin, sulindac, etodolac, mefenamic acid, meclofenamate sodium, tolmetin, ketorolac, dichlofenac, ibuprofen, naproxen, naproxen sodium, fenoprofen, ketoprofen, flurbinprofen, oxaprozin, piroxicam, meloxicam, ampiroxicam, droxicam, pivoxicam, tenoxicam, nabumetome, phenylbutazone, oxyphenbutazone, antipyrine, aminopyrine, apazone and nimesulide; leukotriene antagonists including, but not limited to, zileuton, aurothioglucose, gold sodium thiomalate and auranofin; steroids including, but not limited to, alclometasone diproprionate, amcinonide, beclomethasone dipropionate, betametasone, betamethasone benzoate, betamethasone diproprionate, betamethasone sodium phosphate, betamethasone valerate, clobetasol proprionate, clocortolone pivalate, hydrocortisone, hydrocortisone derivatives, desonide, desoximatasone, dexamethasone, flunisolide, flucoxinolide, flurandrenolide, halcinocide, medrysone, methylprednisolone, methprednisolone acetate, methylprednisolone sodium succinate, mometasone furoate, paramethasone acetate, prednisolone, prednisolone acetate, prednisolone sodium phosphate, prednisolone tebuatate, prednisone, triamcinolone, triamcinolone acetonide, triamcinolone diacetate, and triamcinolone hexacetonide; and other anti-inflammatory agents including, but not limited to, methotrexate, colchicine, allopurinol, probenecid, sulfinpyrazone and benzbromarone.
The compounds of the invention can be formulated in combination with another antiviral agent. Useful antiviral agents include, but are not limited to, protease inhibitors, nucleoside reverse transcriptase inhibitors, non-nucleoside reverse transcriptase inhibitors and nucleoside analogs. The antiviral agents include but are not limited to zidovudine, acyclovir, gangcyclovir, vidarabine, idoxuridine, trifluridine, and ribavirin, as well as foscarnet, amantadine, rimantadine, saquinavir, indinavir, amprenavir, lopinavir, ritonavir, a-interferons; adefovir, clevadine, entecavir, pleconaril.
The compounds of the invention can be formulated in combination with an immunomodulatory agent. Immunomodulatory agents include, but are not limited to, methothrexate, leflunomide, cyclophosphamide, cyclosporine A, mycophenolate mofetil, rapamycin (sirolimus), mizoribine, deoxyspergualin, brequinar, malononitriloamindes (e.g., leflunamide), T cell receptor modulators, and cytokine receptor modulators, peptide mimetics, and antibodies (e.g., human, humanized, chimeric, monoclonal, polyclonal, Fvs, ScFvs, Fab or F(ab)2 fragments or epitope binding fragments), nucleic acid molecules (e.g., antisense nucleic acid molecules and triple helices), small molecules, organic compounds, and inorganic compounds. Examples of T cell receptor modulators include, but are not limited to, anti-T cell receptor antibodies (e.g., anti-CD4 antibodies (e.g., cM-T412 (Boeringer), IDEC-CE9.1® (IDEC and SKB), mAB 4162W94, Orthoclone and OKTcdr4a (Janssen-Cilag)), anti-CD3 antibodies (e.g., Nuvion (Product Design Labs), OKT3 (Johnson & Johnson), or Rituxan (IDEC)), anti-CD5 antibodies (e.g., an anti-CD5 ricin-linked immunoconjugate), anti-CD7 antibodies (e.g., CHH-380 (Novartis)), anti-CD8 antibodies, anti-CD40 ligand monoclonal antibodies (e.g., IDEC-131 (IDEC)), anti-CD52 antibodies (e.g., CAMPATH 1H (Ilex)), anti-CD2 antibodies, anti-CD11 a antibodies (e.g., Xanelim (Genentech)), and anti-B7 antibodies (e.g., IDEC-114 (IDEC)) and CTLA4-immunoglobulin. Examples of cytokine receptor modulators include, but are not limited to, soluble cytokine receptors (e.g., the extracellular domain of a TNF-α. receptor or a fragment thereof, the extracellular domain of an IL-1β. receptor or a fragment thereof, and the extracellular domain of an IL-6 receptor or a fragment thereof), cytokines or fragments thereof (e.g., interleukin (IL)-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-15, TNF-α, interferon (IFN)-α, IFN-β., IFN-γ, and GM-CSF), anti-cytokine receptor antibodies (e.g., anti-IFN receptor antibodies, anti-IL-2 receptor antibodies (e.g., Zenapax (Protein Design Labs)), anti-IL-4 receptor antibodies, anti-IL-6 receptor antibodies, anti-IL-10 receptor antibodies, and anti-IL-12 receptor antibodies), anti-cytokine antibodies (e.g., anti-IFN antibodies, anti-TNF-α antibodies, anti-IL-1β antibodies, anti-IL-6 antibodies, anti-IL-8 antibodies (e.g., ABX-IL-8 (Abgenix)), and anti-IL-12 antibodies).
The compounds of the invention can be formulated in combination with cytokines. Examples of cytokines include, but are not limited to, interleukin-2 (IL-2), interleukin-3 (IL-3), interleukin-4 (IL-4), interleukin-5 (IL-5), interleukin-6 (IL-6), interleukin-7 (IL-7), interleukin-9 (IL-9), interleukin-10 (IL-10), interleukin-12 (IL-12), interleukin 15 (IL-15), interleukin 18 (IL-18), platelet derived growth factor (PDGF), erythropoietin (Epo), epidermal growth factor (EGF), fibroblast growth factor (FGF), granulocyte macrophage stimulating factor (GM-CSF), granulocyte colony stimulating factor (G-CSF), macrophage colony stimulating factor (M-CSF), prolactin, and interferon (IFN), e.g., IFN-α, and IFN-γ).
The compounds of the invention can be formulated in combination with hormones. Examples of hormones include, but are not limited to, luteinizing hormone releasing hormone (LHRH), growth hormone (GH), growth hormone releasing hormone, ACTH, somatostatin, somatotropin, somatomedin, parathyroid hormone, hypothalamic releasing factors, insulin, glucagon, enkephalins, vasopressin, calcitonin, heparin, low molecular weight heparins, heparinoids, synthetic and natural opioids, insulin thyroid stimulating hormones, and endorphins.
The compounds of the invention can be formulated in combination with β-interferons which include, but are not limited to, interferon β-1a and interferon β-1b.
The compounds of the invention can be formulated in combination with an absorption enhancer, particularly those which target the lymphatic system, including, but not limited to sodium glycocholate; sodium caprate; N-lauryl-D-maltopyranoside; EDTA; mixed micelle; and those reported in Muranishi Crit. Rev. Ther. Drug Carrier Syst., 7-1-33, which is hereby incorporated by reference in its entirety. Other known absorption enhancers can also be used. Thus, the invention also encompasses a pharmaceutical composition comprising one or more sulfated polysaccharides of the invention and one or more absorption enhancers.
The additional therapeutic agent can act additively or, more preferably, synergistically. In a preferred embodiment, a composition comprising a compound of the invention is administered concurrently with the administration of another therapeutic agent, which can be part of the same composition or in a different composition from that comprising the compounds of the invention. In another embodiment, a compound of the invention is administered prior to or subsequent to administration of another therapeutic agent. In a separate embodiment, a compound of the invention is administered to a patient who has not previously undergone or is not currently undergoing treatment with another therapeutic agent, particularly an antiviral agent.

Oral Dosage Forms

A compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof and compositions comprising a compound of the invention that are suitable for oral administration can be presented as discrete dosage forms, such as, but are not limited to, tablets (e.g., chewable tablets), caplets, capsules, and liquids (e.g., flavored syrups). Such dosage forms contain predetermined amounts of active ingredients, and may be prepared by methods of pharmacy well known to those skilled in the art. See generally, Remington's Pharmaceutical Sciences, 18th ed., Mack Publishing, Easton Pa. (1990).
Typical oral dosage forms of the invention are prepared by combining the active ingredient(s) in an intimate admixture with at least one excipient according to conventional pharmaceutical compounding techniques. Excipients can take a wide variety of forms depending on the form of preparation desired for administration. For example, excipients suitable for use in oral liquid or aerosol dosage forms include, but are not limited to, water, glycols, oils, alcohols, flavoring agents, preservatives, and coloring agents. Examples of excipients suitable for use in solid oral dosage forms (e.g., powders, tablets, capsules, and caplets) include, but are not limited to, starches, sugars, micro-crystalline cellulose, diluents, granulating agents, lubricants, binders, and disintegrating agents.
Because of their ease of administration, tablets and capsules represent the most advantageous oral dosage unit forms, in which case solid excipients are employed. If desired, tablets can be coated by standard aqueous or nonaqueous techniques. Such dosage forms can be prepared by any of the methods of pharmacy. In general, pharmaceutical compositions and dosage forms are prepared by uniformly and intimately admixing the active ingredients with liquid carriers, finely divided solid carriers, or both, and then shaping the product into the desired presentation if necessary.
For example, a tablet can be prepared by compression or molding. Compressed tablets can be prepared by compressing in a suitable machine the active ingredients in a free-flowing form such as powder or granules, optionally mixed with an excipient. Molded tablets can be made by molding in a suitable machine a mixture of the powdered compound moistened with an inert liquid diluent.
Examples of excipients that can be used in oral dosage forms of the invention include, but are not limited to, binders, fillers, disintegrants, and lubricants. Binders suitable for use in pharmaceutical compositions and dosage forms include, but are not limited to, corn starch, potato starch, or other starches, gelatin, natural and synthetic gums such as acacia, sodium alginate, alginic acid, other alginates, powdered tragacanth, guar gum, cellulose and its derivatives (e.g., ethyl cellulose, cellulose acetate, carboxymethyl cellulose calcium, sodium carboxymethyl cellulose), polyvinyl pyrrolidone, methyl cellulose, pre-gelatinized starch, hydroxypropyl methyl cellulose, (e.g., nos. 2208, 2906, 2910), microcrystalline cellulose, and mixtures thereof.
Examples of fillers suitable for use in the pharmaceutical compositions and dosage forms disclosed herein include, but are not limited to, talc, calcium carbonate (e.g., granules or powder), microcrystalline cellulose, powdered cellulose, dextrates, kaolin, mannitol, silicic acid, sorbitol, starch, pre-gelatinized starch, and mixtures thereof. The binder or filler in pharmaceutical compositions of the invention is typically present in from about 50 to about 99 weight percent of the pharmaceutical composition or dosage form.
Suitable forms of microcrystalline cellulose include, but are not limited to, the materials sold as AVICEL-PH-101, AVICEL-PH-103 AVICEL RC-581, AVICEL-PH-105 (available from FMC Corporation, American Viscose Division, Avicel Sales, Marcus Hook, Pa.), and mixtures thereof. A specific binder is a mixture of microcrystalline cellulose and sodium carboxymethyl cellulose sold as AVICEL RC-581. Suitable anhydrous or low moisture excipients or additives include AVICEL-PH-103.™ and Starch 1500 LM.
Disintegrants are used in the compositions of the invention to provide tablets that disintegrate when exposed to an aqueous environment. Tablets that contain too much disintegrant may disintegrate in storage, while those that contain too little may not disintegrate at a desired rate or under the desired conditions. Thus, a sufficient amount of disintegrant that is neither too much nor too little to detrimentally alter the release of the active ingredients should be used to form solid oral dosage forms of the invention. The amount of disintegrant used varies based upon the type of formulation, and is readily discernible to those of ordinary skill in the art. Typical pharmaceutical compositions comprise from about 0.5 to about 15 weight percent of disintegrant, specifically from about 1 to about 5 weight percent of disintegrant.
Disintegrants that can be used in pharmaceutical compositions and dosage forms of the invention include, but are not limited to, agar-agar, alginic acid, calcium carbonate, microcrystalline cellulose, croscarmellose sodium, crospovidone, polacrilin potassium, sodium starch glycolate, potato or tapioca starch, pre-gelatinized starch, other starches, clays, other algins, other celluloses, gums, and mixtures thereof
Lubricants that can be used in pharmaceutical compositions and dosage forms of the invention include, but are not limited to, calcium stearate, magnesium stearate, mineral oil, light mineral oil, glycerin, sorbitol, mannitol, polyethylene glycol, other glycols, stearic acid, sodium lauryl sulfate, talc, hydrogenated vegetable oil (e.g., peanut oil, cottonseed oil, sunflower oil, sesame oil, olive oil, corn oil, and soybean oil), zinc stearate, ethyl oleate, ethyl laureate, agar, and mixtures thereof. Additional lubricants include, for example, a syloid silica gel (AEROSIL 200, manufactured by W. R. Grace Co. of Baltimore, Md.), a coagulated aerosol of synthetic silica (marketed by Degussa Co. of Plano, Tex.), CAB-O-SIL (a pyrogenic silicon dioxide product sold by Cabot Co. of Boston, Mass.), and mixtures thereof. If used at all, lubricants are typically used in an amount of less than about 1 weight percent of the pharmaceutical compositions or dosage forms into which they are incorporated.

Parenteral and Intravascular Dosage Forms

Parenteral and intravascular dosage forms can be administered to patients by various routes including, but not limited to, subcutaneous, intravenous (including bolus injection and constant infusion), intramuscular, and intraarterial. Because their administration typically bypasses patients' natural defenses against contaminants, parenteral and intravascular dosage forms are preferably sterile or capable of being sterilized prior to administration to a patient. Examples of parenteral dosage forms include, but are not limited to, solutions ready for injection, dry products (including, but not limited to lyophilized powders, pellets, and tablets) ready to be dissolved or suspended in a pharmaceutically acceptable vehicle for injection, suspensions ready for injection, and emulsions.
Suitable vehicles that can be used to provide parenteral dosage forms of the invention are well known to those skilled in the art. Examples include, but are not limited to: Water for Injection USP; aqueous vehicles such as, but not limited to, Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection, and Lactated Ringer's Injection; water-miscible vehicles such as, but not limited to, ethyl alcohol, polyethylene glycol, and polypropylene glycol; and non-aqueous vehicles such as, but not limited to, corn oil, cottonseed oil, peanut oil, sesame oil, ethyl oleate, isopropyl myristate, and benzyl benzoate.
Compounds that increase the solubility of one or more of the active ingredients disclosed herein can also be incorporated into the parenteral dosage forms of the invention.
For intravascular administration, for instance by direct injection into the blood vessel, or surrounding area, it may be desirable to administer the compositions locally to the area in need of treatment. This can be achieved, for example, by local infusion during surgery, by injection, by means of a catheter, or by means of an implant, said implant being of a porous, non-porous, or gelatinous material, including membranes, such as silastic membranes, or fibers. A suitable such membrane is Gliadel® provided by Guilford Pharmaceuticals Inc.

Transdermal, Topical, and Mucosal Dosage Forms

Transdermal, topical, and mucosal dosage forms of the invention include, but are not limited to, ophthalmic solutions, sprays, aerosols, creams, lotions, ointments, gels, solutions, emulsions, suspensions, or other forms known to one of skill in the art. See, e.g., Remington's Pharmaceutical Sciences, 16th and 18th eds., Mack Publishing, Easton Pa. (1980 & 1990); and Introduction to Pharmaceutical Dosage Forms, 4th ed., Lea & Febiger, Philadelphia (1985). Dosage forms suitable for treating mucosal tissues within the oral cavity can be formulated as mouthwashes or as oral gels. Further, transdermal dosage forms include “reservoir type” or “matrix type” patches, which can be applied to the skin and worn for a specific period of time to permit the penetration of a desired amount of active ingredients.
Suitable excipients (e.g., carriers and diluents) and other materials that can be used to provide transdermal, topical, and mucosal dosage forms encompassed by this invention are well known to those skilled in the pharmaceutical arts, and depend on the particular tissue to which a given pharmaceutical composition or dosage form will be applied. With that fact in mind, typical excipients include, but are not limited to, water, acetone, ethanol, ethylene glycol, propylene glycol, butane-1,3-diol, isopropyl myristate, isopropyl palmitate, mineral oil, and mixtures thereof to form lotions, tinctures, creams, emulsions, gels or ointments, which are non-toxic and pharmaceutically acceptable. Moisturizers or humectants can also be added to pharmaceutical compositions and dosage forms if desired. Examples of such additional ingredients are well known in the art. See, e.g., Remington's Pharmaceutical Sciences, 16th and 18th eds., Mack Publishing, Easton Pa. (1980 & 1990).
Depending on the specific tissue to be treated, additional components may be used prior to, in conjunction with, or subsequent to treatment with active ingredient of the invention. For example, penetration enhancers can be used to assist in delivering the active ingredients to the tissue. Suitable penetration enhancers include, but are not limited to: acetone; various alcohols such as ethanol, oleyl, and tetrahydrofuryl; alkyl sulfoxides such as dimethyl sulfoxide; dimethyl acetamide; dimethyl formamide; polyethylene glycol; pyrrolidones such as polyvinylpyrrolidone; Kollidon grades (Povidone, Polyvidone); urea; and various water-soluble or insoluble sugar esters such as Tween 80 (polysorbate 80) and Span 60 (sorbitan monostearate).
The pH of a pharmaceutical composition or dosage form, or of the tissue to which the pharmaceutical composition or dosage form is applied, may also be adjusted to improve delivery of one or more active ingredients. Similarly, the polarity of a solvent carrier, its ionic strength, or tonicity can be adjusted to improve delivery. Compounds such as stearates can also be added to pharmaceutical compositions or dosage forms to advantageously alter the hydrophilicity or lipophilicity of one or more active ingredients so as to improve delivery. In this regard, stearates can serve as a lipid vehicle for the formulation, as an emulsifying agent or surfactant, and as a delivery-enhancing or penetration-enhancing agent. Different salts, hydrates or solvates of the active ingredients can be used to further adjust the properties of the resulting composition.
Although methods and materials similar or equivalent to those described herein can be used in the practice of the present invention, preferred methods and materials are described below. The materials, methods, and examples are illustrative only and not intended to be limiting. Other features and advantages of the invention will be apparent from the detailed description and from the claims.

Kits

This invention therefore encompasses kits which, when used by the medical practitioner, can simplify the identification of subjects and the administration of appropriate amounts of a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof to a patient.
A typical kit of the invention comprises one or more unit dosage forms of a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof, and instructions for identification of a subject.
Kits of the invention can further comprise devices that are used to administer a compound of the invention or a pharmaceutically acceptable salt, solvate or hydrate thereof. Examples of such devices include, but are not limited to, intravenous cannulation devices, syringes, drip bags, patches, topical gels, pumps, containers that provide protection from photodegradation, autoinjectors, and inhalers.
Kits of the invention can further comprise pharmaceutically acceptable vehicles that can be used to administer one or more active ingredients. For example, if an active ingredient is provided in a solid form that must be reconstituted for parenteral administration, the kit can comprise a sealed container of a suitable vehicle in which the active ingredient can be dissolved to form a particulate-free sterile solution that is suitable for parenteral administration. Examples of pharmaceutically acceptable vehicles include, but are not limited to: Water for Injection USP; aqueous vehicles such as, but not limited to, Sodium Chloride Injection, Ringer's Injection, Dextrose Injection, Dextrose and Sodium Chloride Injection, and Lactated Ringer's Injection; water-miscible vehicles such as, but not limited to, ethyl alcohol, polyethylene glycol, and polypropylene glycol; and non-aqueous vehicles such as, but not limited to, corn oil, cottonseed oil, peanut oil, sesame oil, ethyl oleate, isopropyl myristate, and benzyl benzoate.
All documents mentioned herein are incorporated herein by reference in their entirety.

EXAMPLES

In order that the invention may be more fully understood, the following examples are provided. It should be understood that these examples are for illustrative purposes only and are not to be construed as limiting the invention in any way.

General Experimental Methodology

1. To identify potent and selective small molecule modulators of MCL-1, a small molecule binding screen by competitive fluorescence polarization assay was conducted. Small molecules were screened in parallel against the FITC-MCL-1 SAHB/MCL-1 ΔNΔC interaction and the FITC-BAD BH3/BCL-X_L.ΔC interaction. Those compounds that preferentially disrupted the FITC-MCL-1 SAH13/MCL-1ΔNΔC interaction were advanced to secondary screening analyses.
2. A series of confirmatory binding assays were performed. First, the competitive binding assay using FITC-MCL-1 SAHB/MCL-1ΔNΔC was repeated using dose-response analysis to confirm dose-responsive binding and determine small molecule K_ivalues. Subsequently specificity analysis was performed by competitive fluorescence polarization binding assay of small molecules against the interactions of FITC-BID BH3 in combination with MCL-1ΔNΔC, BCL-2ΔC, BCL-X_L.ΔC, BCL-wΔC, and BFL1/A1ΔC. Small molecules exhibiting high fidelity specificity for MCL-1ΔNΔC over the other anti-apoptotic proteins were advanced to SAR, binding site, and functional analysis. Docking analysis was performed to confirm the compatibility of small molecule structure with an energetically favorable docking site at the structurally defined (i.e. x-ray crystallography) BH3-binding pocket of MCL-1ΔNΔC. Dilutional assays were performed to distinguish between non-covalent and covalent MCL-1 binders. These studies identified a series of covalent interactors; for example, a novel site of interaction for inhibiting MCL-1 binding activity was identified based on covalent modification of MCL-1 by the molecule at cysteine 286. Finally, selective MCL-1 inhibitors were tested in a BAX-mediated liposomal release assay to evaluate their capacity to block the inhibitory/anti-apoptotic activity of MCL-1.
3. Small molecule modulators of MCL-1 were then tested in a cellular apoptosis sensitization assay using OPM2 cells exposed to subcytotoxic doses of TRAIL in the presence or absence of serial dilutions of small molecule. Sensitization activity was also confirmed by use of CalcuSyn analysis of combination treatments.

Methods

SAHB Synthesis.

Hydrocarbon-stapled peptides corresponding to BCL-2 family BH3 domains and their FITC-.β.Ala derivatives were synthesized, purified, and characterized using previously described methodologies^24,27,29.

Anti-Apoptotic Protein Preparation.

Recombinant and tagless MCL-1ΔNΔC, BCL-2 ΔC, BCL-XLΔC, BCL-wΔC, and BFL1/A1ΔC were produced using previously described methods^27,29,31.

Small Molecule Screening.

Small molecule screens were performed at the Institute for Chemistry and Cellular Biology at Harvard Medical School and employed commercial libraries (Asinex, Chembridge, ChemDiv, Enamine, Life Chemicals, and Maybridge). A high-throughput competitive FP binding assay was employed to screen for small molecules that disrupted the interaction between FITC-MCL-1 SAHB (15 nM) and MCL-1ΔNΔC (45 nM). MCL-1ΔNΔC was expressed and purified by FPLC and delivered by automated liquid handler to 384 well plates, followed by addition of small molecule libraries. After a 15 minute incubation at room temperature, FITC-MCL-1 SAHB (15 nM) was added to each well by liquid handler and FP read at equilibrium (e.g. 1 hr). Small molecule hits were re-examined in this assay using serial dilutions of the compounds to confirm dose-responsive inhibition of FITC-MCL-1 SAHB binding.

Confirmatory Binding Analyses.

The most potent hits were advanced to rigorous quantification of binding activity and specificity. First, serial dilutions of small molecule in triplicate were mixed with FITC-MCL-1 SAHB (15 nM), followed by addition to 384-well black Costar plates containing MCL-1ΔNΔC (45 nM) diluted in binding buffer (50 mM Tris, 100 mM NaCl, 0.0625% CHAPS, pH 8.0). The plates were incubated in the dark at room temp until equilibrium was reached (i.e. stabilization of binding isotherms) and FP (mP units) determined using a microplate reader (e.g. Spectramax). K, values were calculated by nonlinear regression analysis of dose-response curves using Prism software (Graphpad). Small molecule hits were then tested for their ability to dissociate FITC-BAK BH3 from MCL-1ΔNΔC in a competitive FP assay, performed as described above except that small molecule dilutions were added to a solution of FITC-BAK BH3 (25 nM) and MCL-1ΔNΔC (250 nM) to simulate a physiologic displacement of pro-apoptotic BAK from the inhibitory MCL-1 protein. For rigorous specificity analysis, the identical competitive FP-type experiment was performed except that serial dilutions of small molecule hits were mixed with the pan-anti-apoptotic binder FITC-BID BH3 (15 nM), followed by addition to plates containing either MCL-1ΔNΔC, BCL-2ΔC, BCL-X_L.ΔC, BCL-wΔC, or BFL1/A1ΔC. We used pGEX vectors to express GST-MCL-1ΔNΔC, BCL-2ΔC, BCL-X_L.ΔC, BCL-wΔC, and BFL1/A1ΔC, followed by thrombin cleavage and FPLC-based gel filtration chromatography. Of note, the C-terminal α-helix was deleted from each of these constructs to facilitate protein expression and purification; an additional N-terminal deletion of MCL-1 was performed to further enhance expression, purity, and stability. FP analysis was performed as above and those molecules showing exclusive binding activity for MCL-1ΔNΔC were advanced to structural docking and functional testing.

Dilution Assay.

MCL-1ΔNΔC (2 μM, 500 mL) was incubated with compound (at a ratio well above each previously determined EC₅₀value) for 1 hour at room temperature in FP buffer (100 mM NaCl, 50 nM Tris, pH 8). A small sample was taken as a pre-dilution control. Compound-treated protein and unmodified protein were then diluted to a volume of 20 mL, and subsequently re-concentrated to 500 mL using 10K centrifugal filter units (Amicon). FP binding analysis was performed as described above by adding serial dilutions of compound-modified MCL-1 and unmodified MCL-1, both before and after dilution, followed by FITC-BID BH3 (15 nM) to a 96-well black flat bottom plate (Costar). FP measurements and analyses are then performed as described above.

Identification of Covalent Modification Site by Mass Spectrometry.

MCL-1ΔNΔC (90 μM) was incubated with a 1:1.25 ratio of compound for 2 hours at room temperature in 150 mM NaCl, 50 mM Tris, pH 7.4. Excess compound was removed by gel filtration and the protein was digested with trypsin overnight at 37° C. Peptides were analyzed by nano-LC/EST/MS using a vented column assembly as described (Ficarro et al., 2009)³⁴. Briefly, peptides were injected using an autosampler and HPLC (Waters NanoAcquity) onto a self-packed precolumn (4 cm, 100 μm I.D., POROS10R2, Applied Biosystems) and gradient eluted (0-30% B in 20 minutes, A=0.2 M acetic acid in water, B=acetonitrile with 0.2M acetic acid) to the resolving column (self-packed 30 μm I.D., 12 cm of 5 μm Monitor C18, Column Engineering) and introduced to the mass spectrometer (Thermo Fisher LTQ-Orbitrap XL) via ESI (spray voltage=2.2 kV). The top 8 most abundant precursors in each MS scan (image current detection, resolution=30,000) were subjected to CAD (electron multiplier detection, collision energy=35%). A separate targeted nano-LC/EST/NIS experiment was performed with compound-modified peptide (e.g. TEN QES*CIEPLAESITDVLVR [*C=modified cysteine)]), which was subjected to HCD (higher energy collisionally activated dissociation).

Liposomal Release Assay.

Liposomes are prepared from a mixture of lipids that reflect the composition of the outer mitochondrial membrane as previously described in detail (Pitter et al., 2008)³¹. Aliquots of mixed lipids (1 mg total) are stored in glass at −20° C. under nitrogen, and before use, resuspended in liposome assay buffer (10 mM HEPES, 200 mM KCl, 1 mM MgCl₂, pH 7) with 12.5 mM of the fluorescent dye ANTS (8-aminonaphthalene-1,3,6-trisulfonic acid, disodium salt) and 45 mM of the quencher DPX (p-xylene-bis-pyridinium bromide). The resulting slurry is vortexed for 10 minutes and freeze-thawed five times alternating between liquid nitrogen and a 40° C. water bath. The solution is then passed through an Avanti Mini-Extruder Set (#610000) equipped with a 100-nm filter, followed by passage through a Sepharose column (GE Healthcare) to remove residual ANTS/DPX. The lipsomes are brought up to a volume of 3 mL to produce a final liposome stock. For the liposomal release assay, a total volume of 30 μL is used in 384 well black flat bottom plates (Costar), and baseline fluorescence measurements of 8 μL liposomes are made for 10 minutes using the Tecan Infinite M1000 (excitation: 355 nm, emission: 520 nm). Following the baseline read, recombinant MCL-1ΔNΔC pre-incubated with a 1:1 ratio of compound is added to the liposomes. Next, 20 nM caspase-cleaved mouse BID (R&D systems) and 250 nM purified recombinant monomeric BAX is added, and fluorescence measurements (F) are recorded every minute from time zero (F0) until the release readings plateau. The liposomes are then quenched with 1% Triton X-100 (100% release; F100), and percent ANTS/DPX release is calculated as ((F−F0)/(F100−F0))×100.

Cytochrome c Release Assays.

Mouse liver mitochondria (0.5 mg/mL) are isolated and release assays performed as described³¹. Mitochondria are incubated with a serial dilution of MCL-1 targeting small molecule, singly or in combination with BID BH3, and after 40 minutes, the pellet and supernatant fractions are isolated and cytochrome c quantitated using a colorimetric ELISA assay (R&D Systems). Percent cytochrome c released into the supernatant (% cytoc_sup) from releasable mitochondrial pools was calculated according to the following equation: % cytocl=[(cytoc_sup−cytoc_backgr)/(cytoc_total−cytoc_backgr)]*100, where background release represents cytochrome c detected in the supernatant of vehicle-treated (1% DMSO) samples and total release represents cytochrome c measured in 1% Triton-X 100 treated samples. All experimental conditions are also tested on Bak^−/−mitochondria to ensure that the observed cytochrome c release from wild-type mitochondria derives from BAK activation.

Immunoprecipitation Assay.

MCL-1-expressing cancer cells (10×10⁶) are incubated with the MCL-1 targeting small molecule or vehicle in serum-free media at 37° C. for 4 hours, followed by serum replacement for an additional 6 hours. After cellular lysis in 50 mM Tris (pH 7.4), 150 mM NaCl, 1 mM EDTA, 1 mM DTT, 0.5% NP40 and complete protease inhibitor pellet, cellular debris is pelleted at 14,000 g for 10 minutes at 4° C. The supernatant is exposed to pre-equilibrated protein A/G sepharose beads and the pre-cleared supernatant subsequently incubated with anti-MCL-1 antibody for 1.5 hours at 4° C., followed by the addition of protein A/G sepharose beads for 1 hour. The beads are pelleted and washed with lysis buffer for 10 minutes at 4° C. The washed bead are then pelleted, heated to 90° C. for 10 minutes in SDS loading buffer, analyzed by SDS/PAGE, and then immunoblotted for MCL-1 and BAK.

Crystallography.

Crystallization conditions for lead small molecule-MCL-1ΔNΔC complexes are screened using 96-well sitting drop plates set up using a Phoenix crystallization robot. Initial conditions include HT Index Screen, JSCG+ Suite, and Pro-Complex Suite. Screening around the best hit, including varying pH, salt, and detergent concentrations, are performed to identify the best condition for crystal growth. Once generated, the crystals are removed, washed in the crystallization buffer, and subjected to mass spectroscopy to verify the presence of compound and protein within the crystal. The crystal is then soaked in cyroprotectant, flash frozen, and stored in liquid nitrogen. Suitable crystals are examined at the Argonne National Laboratory synchrotron facility. Phases are obtained by molecular replacement followed by data analysis and refinement (Phaser, Phenix, and Coots software).

Cellular Apoptosis Induction Assays.

Small molecule inhibitors of MCL-1 were screened in MCL-1-expressing cancer cell lines, such as OPM-2 (multiple myeloma) cells. The cells are treated with the small molecule MCL-1 inhibitor, alone or in combination with subtherapeutic pro-apoptotic stimuli (e.g. TRAIL, Fas ligand, ABT-737), and then cell viability is measured at 48 hours by MTT assay performed according to the manufacturer's protocol (Roche) and quantitated by an ELISA microplate reader (Biorad). IC₅₀values were determined by nonlinear regression analysis using Prism software (Graphpad). Small molecules that decrease cell viability are then screened for cellular apoptosis induction by annexin V binding and FACS analysis, and by cell fractionation-based mitochondrial cytochrome c release, as described²⁸. Apoptosis is also correlated with in situ dissociation of the MCL-1/BAK complex (immunoprecipitation) performed as described above. As an additional measure of small molecule MCL-1 specificity, the identical experiments are conducted on wild-type vs. Mcl-1^−/− MEFs, to explicitly link the selective MCL-1 targeting capacity of the small molecules to sensitization of apoptosis. The caspase-dependency of small molecule activity is also confirmed by monitoring for blockade of activity upon co-treatment with the pan-capase inhibitor Z-VAD.

Pharmacokinetic Analyses.

Lead small molecules undergo pharmacokinetic (PK) analysis in mice, performed in conjunction with the DF/HCC Clinical Pharmacology Core. LC/MS-based analytical assays are developed in order to detect and quantify compound levels in plasma. For PK analysis, small molecules (e.g. 10, 50, 100 mg/kg) are injected by tail vein or intraperitoneally into male C57/BL6 mice. Blood samples are withdrawn by retro-orbital bleed at various time points and plasma isolated for compound quantification, followed by calculation of plasma half-life, peak plasma levels, total plasma clearance, and apparent volume of distribution. Small molecules that exhibit selective MCL-1 targeting in cells and exhibit a favorable pharmacokinetic profile re advanced to in vivo testing.

In Vivo Efficacy Studies.

Small molecule-sensitive cancer cell lines are retrovirally transduced to achieve stable luciferase expression (pMMP-LucNeo) and transplanted into SCID beige mice as previously described^27,32. Initial xenograft studies examine 5 mouse cohorts (n=10), treated with either vehicle alone, low or high dose small molecule alone, or low/high dose small molecule in combination with subtherapeutic dosing of pro-apoptotic stimuli (e.g. TRAIL, ABT-737, doxorubicin, etoposide, dexamethasone). Starting on experimental day 1, mice receive a once daily tail injection of small molecule (e.g. 25 or 100 mg/kg, with or without combination treatment). For alternate day in vivo tumor imaging, mice are anesthetized with inhaled isoflurane and treated concomitantly with intraperitoneal injection of D-luciferin. Photonic emission is imaged (2 min exposure) using a Xenogen In Vivo Imaging System and total body bioluminescence quantified by the integration of photonic flux (photons/sec) using Xenogen's Living Image Software. The survival distributions of experimental mice are determined using the Kaplan-Meier method and compared using the log-rank test. The Fisher's exact test is used to compare the proportion of mice who fail treatment, where treatment failure is defined as progression or death, and success as stable disease or regression. If a treatment response is observed with a particular small molecule, three additional cohorts, treated with either vehicle, small molecule, or small molecule combination will be used for pharmacodynamic studies in which pro-apoptotic activity is evaluated in tissues by TUNEL and activated caspase-3 immunohistochemical staining.

EXAMPLES

Identification of MCL-1 Selective Small Molecules by a Competitive Fluorescence Polarization Binding Assay Using FITC-MCL-1 SAHB and MCL-1ΔNΔC

A high-throughput competitive FP binding assay was employed to screen for small molecules that disrupted the interactions between FITC-MCL-1 SAHB/MCL-1ΔNΔC and FITC-BAD BH3/BCL-X_LΔC (FIG. 1). Compounds were ranked based upon their selectivity for MCL-1 ΔNΔC over BCL-X_L.ΔC targeting, and tabulated (see Table 1 (including Subtables Table 1-A through Table 1-P)).

The Structures of Small Molecule/MCL-1 Complexes Provide a Template for Refining MCL-1 Binding Activity and Specificity.

Using the crystal structure of MCL-1ΔNΔC, the identified small molecules were docked onto the BH3-binding pocket of MCL-1ΔNΔC to analyze the location and energetic favorability of interaction. The compounds covered discrete subregions of BH3-binding pocket topography (FIG. 2), providing a blueprint for engineering selective, larger molecules that incorporate combinations of molecules or their subfragments to engage the complex and extended BH3-binding surface of MCL-1.
Subclassification of Selective MCL-1 Inhibitors Based on Non-Covalent Vs. Covalent Interactions.
To examine the mechanism of small molecule binding to MCL-1, the compounds were subjected to a rapid dilution assay (FIG. 2C). Briefly, MCL-1ΔNΔC was pre-incubated with the small molecule inhibitors prior to dilution with buffer. The solution was concentrated to its original volume and fluorescence polarization was performed. Compounds that bind covalently will remain bound to the protein, whereas compounds that bind reversibly will be exchanged upon dilution. As a positive control, the rapid dilution assay confirmed that gossypol (1570G15) bound reversibly to MCL-1ΔNΔC (FIG. 2C, top panel). In contrast, 1725P16 and 1597E07 failed to exchange upon dilution, indicating that the compounds bind and covalently modified MCL-1ΔNΔC (FIG. 2C, middle, bottom panels).

Identification of a Novel Interaction Site for MCL-1 Inhibition Based on C286 Engagement.

To localize sites of covalent modification, small molecule-treated MCL-1ΔNΔC (e.g. 1929A19) was subjected to mass spectrometry. An additional MALDI peak was observed for small molecule-treated protein, with the increase in mass corresponding to the molecular weight of the covalently tethered compound. The MCL-1ΔNΔC-adduct was further subjected to tandem MS/MS, which revealed cysteine 286 as the site of modification for 1929A19 (FIG. 2D). Importantly, cysteine 286 is not located at the canonical BH3 binding pocket (FIG. 2D), indicating that engagement of this novel binding site can allosterically regulate MCL-1's anti-apoptotic/BH3-binding activity. To confirm the functional importance of C286 engagement, a C286S construct of MCL-1ΔNΔC was generated by site-direct mutagenesis and small molecule binding activity was compared in competitive FP assays using FITC-BID BH3 and the wild-type and mutant MCL-1ΔNΔC proteins. Whereas 1929A19 and 1616N08 competed with FITC-BID BH3 for MCL-1ΔNΔC binding, the molecules failed to engage the C286S construct of MCL-1ΔNΔC, as demonstrated by the capacity of FITC-BID BH3 to maintain binding activity toward MCL-1ΔNΔC C286S in the presence of the compounds.

Confirmation of Small Molecule Binding Activity and Selectivity by Use of Competitive Binding Assays.

To verify the capacity of the identified small molecules to selectively target MCL-1ΔNΔC, small molecule hits were tested for their differential ability to dissociate FITC-BID BH3 from a panel of anti-apoptotic proteins, including MCL-1ΔNΔC, BCL-2ΔC, BCL-XLΔC, BCL-wΔC, and BFL1/A1ΔC. As exemplified in FIGS. 3 and 4, small molecules identified as MCL-1ΔNΔC selective indeed exhibited preferential displacement of FITC-BID BH3 from MCL-1ΔNΔC compared to the other anti-apoptotic proteins tested.

Structure-Activity Relationship Analysis of Selective MCL-1 Inhibitors.

Chemical derivatives of class A (FIG. 4C) and J (FIG. 4D) molecules demonstrated significant differences in binding activity. Importantly, the five-member thiotriazole ring at position R1 of class A increased binding affinity for MCL-1ΔNΔC compared to smaller, non-aromatic substituents. At the R2 position, aromatic residues were favored with small hydrophobic side chains or hydrogen bond acceptors at the para-position of the phenyl ring. For class J, small aliphatic groups were well tolerated at the R1 position, and the trihydroxyphenyl ring at the R2 position demonstrated superior binding affinity for MCL-1ΔNΔC. Finally, five- or six-member aromatic rings were favored at the R3 position. Specifically, analogs that contained methyl substituents at R3 displayed no activity unless paired with a large aliphatic group at the R1 position.

Small Molecule MCL-1 Binders Sensitize Cancer Cells to Pro-Apoptotic Stimuli.

Cancer cells that depend on MCL-1 for survival were treated with selective small molecule MCL-1ΔNΔC binders in combination with other pro-apoptotic agents to assess for synergistic anti-tumor activity. As exemplified in FIG. 5, small molecule bioactives synergized with TRAIL to kill OPM2 multiple myeloma cells, as assessed by MTT viability assay and by combination treatment analysis using CalcuSyn software.

Selective MCL-1 Inhibitors Block the Anti-Apoptotic Function of MCL-1 in a BAX-Mediated Liposomal Release Assay.

The liposomal release assay is designed to mimic the functional release of mitochondrial cytochrome c by formation BAX-containing pores within the outer mitochondrial. membrane. Here, recombinant full length BAX was incubated with recombinant tBID in the presence or absence of MCL-1ΔNΔC. As demonstrated in FIG. 6, tBID triggered BAX-mediated release of the fluorophore from the liposome in a time-dependent manner. MCL-1ΔNΔC blocked BAX activation, inhibiting fluorophore release. By inhibiting MCL-1ΔNΔC, 1929A19 and 1616N08 dose-responsively re-instated tBID-induced, BAX-mediated liposomal release of the fluorophore, highlighting the capacity of the small molecule MCL-1 inhibitors to block the anti-apoptotic activity of MCL-1.


TABLE 1-A

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	34.13126397	102.3629331	68.231669

	16.68871081	105.3416001	88.652889

	34.54623163	100.760843	66.214611

	35.01128141	106.8345939	71.823312

	56.60157162	106.2747212	49.67315

	10.32290702	104.1661092	93.843202

	1.259544221	90.57802572	89.318482

	27.20036677	100.4228001	73.222433

	3.955080904	101.0243434	97.069262

	41.01271009	100.3606236	59.347914

	32.90443509	97.09434568	64.189911

	5.93536133	98.2573418	82.32198

TABLE 1-B

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	2.332623997	103.4341651	101.1015411

	4.951710591	96.11650485	91.16479426

	19.67020024	96.38730675	76.71710652

	19.74954984	93.16376474	73.4142149

	35.6	98.3	62.7

	36.15465782	91.34577213	551.9111431

TABLE 1-C

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	9.463295931	115.1848233	105.7215274

	−0.3	108.4	108.7

	42.48636709	113.7228826	71.23651547

	27.16644285	93.0177803	65.85133746

	43.7012494	106.4084449	62.70719545

	58.33277892	103.7511722	45.41839332

TABLE 1-D

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	14.6	101.3	86.7

	−2.04714193	75.96629122	78.01343315

	8.332108744	81.17127433	72.83916559

	43.2	109.5	66.3

	35.72624681	99.74101397	64.01476715

	37.6	98.3	60.7

	45.37762426	98.52069172	53.14306746

TABLE 1-E

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	−0.7333720591	80.396769391	81.13014145

	11.72800505	79.877899881	68.14989482

	31.16639478	95.42028511	64.25389033

	38.47471452	101.4501065	61.97539199

	18.74037573	77.59057823	58.85020251

	47.00574838	99.25113873	52.245390351

	53.4905597	105.6295695	52.139009761

	47.953523241	96.90361633	48.95009309

	56.33127545	104.43159921	48.100323781

	55.14812663	103.2306124	48.08248577

	64.63766028	112.7047864	48.0671261

	62.71844661	110.0825659	47.36411929

	40.50995892	86.74650699	46.23654860

	66.09053804	111.9999168	45.90937874

	56.10428305	101.763264	45.65898096

	69.53461354	115.1985743	45.66396079

	68.79611916	114.1804937	45.3847457

TABLE 1-F

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	14.30073607	84.68236855	70.38163248

	25.28012412	92.88964225	67.60951814

	19.17808219	73.82692962	54.64884742

	33.27874504	82.61218664	49.33344159

TABLE 1-G

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	24.59486004	99.32600497	74.73114493

	18.96382387	92.90700473	73.94318087

	15.16614831	84.81906443	69.65291612

	30.48780488	79.68386424	49.19605936

TABLE 1-H

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	−10.5954323	87.16025145	97.75748375

	7.037265168	97.35012677	90.3128616

	3.36867863	86.24446993	82.8757913

	−7.07177814	75.49565787	82.56743601

	20.58823529	102.1918705	81.60363516

	30.19710502	107.6879038	77.4907988

	21.8	98.2	76.4

	15.04465661	89.36779259	74.32313598

	31.4290114	89.23693465	57.80792326

	30.81305821	84.78776478	53.97470658

	36.80576864	89.70132202	52.89555338

	38.82044965	91.59237753	62.77192788

	29.33477056	78.76829966	49.43352911

TABLE 1-I

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	−5.219264716	104.6841563	109.903421

	11.19902121	76.15107324	64.95205204

	25.38058602	86.7447645	61.36417848

	44.3557943	92.23836973	47.88257544

TABLE 1-J

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	19.08127028	95.08543531	76.00416323

	43.51306119	106.90959621	63.39653504;

	39.32183657	100.3628503	61.04101373

	41.8167411	102.1683264	60.35158527

	38.17542436	95.91685226	57.74142791

	45.19897498	102.0166733	56.81769831

	41.985733	98.20470972	56.21897672

	52.01193335	105.6743612	53.6624278

	46.42363385	99.00409172	52.58045787

	39.96352925	92.21643287	52.25290362

	30.59011861	81.34023006	50.75011146

	33.00999412	82.65729799	49.64730387

	51.18862475	99.22340759	48.03478284

	55.45434348	100.8550361	45.4006926

TABLE 1-K

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	2.606828112	96.58770003	93.98087192

	15.57226143	89.44018281	73.86792137

	48.21516581	111.214653	62.9948715

	43.16379248	101.2275149	58.06372239

	13.28219273	66.62503346	53.34284073

	48.95344507	97.58836088	48.63491581

	215.6015433	263.737406	48.13586273

	40.42192793	87.79749734	47.37556941

TABLE 1-L

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	−9.610778443	87.82745228	97.43823072

	19.68883273	102.4094424	82.72060968

	33.27029276	112.3457833	79.07549058

	26.07784431	102.7683663	76.69052194

	19.8	95.8	76.1

	38.57217917	107.8998073	69.32762815

	21.28742515	90.20742087	68.91999572

	23.0	89.9	66.9

	29.45492662	92.21556886	62.76064224

	27.92957859	86.64814815	57.71856956

	38.04746419	92.34466638	55.29720219

	21.54074074	76.08572124	54.54498051

	42.5929832	94.16497422	51.57199103

	39.83535868	91.73339804	51.89803936

	48.7076967	98.89474361	50.1870469

	58.50862999	105.8574397	47.34880968

TABLE 1-M

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	−23.10049446	101.7468716	124.8473661

	−16.27483907	89.94614004	106.2209791

TABLE 1-N

	MCL-1 %	BCL-XL %	Spec
Structure	Bound	Bound	Values

	−65.83063646	102.6892674	168.5199038

	−6.59173964	129.3090909	135.9008305

	−23.10049446	101.7468716	124.8473661

	−30.96202705	88.78573776	119.7477648

	−5.219264716	104.6841563	109.903421

	−0.3	108.4	108.7

	−1.785938876	106.6729323	108.4588712

	−11.55743971	96.56812237	108.1255621

	−16.27483907	89.94614004	106.2209791

	9.463295931	115.1848233	105.7215274

	−7.035327937	98.55501099	105.5903389

	10.7155014	114.7223418	104.0068404

	2.332623997	103.4341651	101.1015411

	14.04124001	112.8657315	98.82449146

	−10.86859971	87.36357022	98.23216992

	−14.50299142	83.61559031	98.11858173

	−10.5954323	87.16205145	97.75748375

	9.610778443	87.82745228	97.43823072

	3.955080904	101.0243434	97.0692625

	−18.5	78.1!	96.6

	2.606828112	96.58770003	93.98087192

	10.32290702	104.1661092	93.84320213

	6.6	99.9	93.2

	4.951710591	96.11650485	91.16479426

	7.037265168	97.35012677	90.3128616

	1.259544221	90.57802572	89.3184815

	14.82516366	103.9217319	89.09656823

	16.68871081	105.3416001	88.65288929

	14.6	101.3	86.7

	−13.00667806	71.10363607	84.11031413

	30.17353579	114.1379598	83.964424

	16.19966207	99.90532748	83.70566541

	9.240186268	92.49338093	83.25319466

	3.36867863	86.24446993	82.8757913

	19.68883273	102.4094424	82.72060968

	20.72333282	103.4206261	82.69729329

	6.516370589	89.09642401	82.58005342

	−7.07177814	75.49565787	82.56743601

	15.93536133	98.2573418	82.32198048

	20.58823529	102.1918705	81.60363516

	−0.733372059	80.39676939	81.13014145

	22.9770388	104.0060981	81.02905928

	11.4	92.2	80.8

	−3.913592369	75.92785571	79.841448081

	21.93834459	101.5900478	79.65170319

	33.27029276	112.3457833	79.07549058

	−2.04714193	75.96629122	78.01343315

	30.19710502	107.6879038	77.4907988

	19.67020024	96.38730675	76.71710652

	13.3744856	90.06707122	76.69258563

	26.07784431	102.7683663	76.69052194

	21.8	98.2	76.4

	17.4	93.7	76.4

	19.8	95.8	76.1

	19.08127208	95.08543531	76.00416323

	21.79034158	97.16842962	75.37808804

	21.55274889	96.34785598	74.79510709

	24.59486004	99.32600497	74.73114493

	15.04465661	89.36779259	74.32313598

	18.96382387	92.90700473	73.94318087

	15.57226143	89.4401828	73.86792137

	19.74954984	93.16376474	73.4142149

	27.20036677	100.4228001	73.22243335

	37.92480367	111.0248078	73.10000413

	30.22510381	103.1419548	72.916851

	8.332108744	81.17127433	72.83916559

	12.58907363	84.89878885	72.30971522

	35.01128141	106.8345939	71.8233125

	42.48636709	113.7228826	71.236515471

	−5.849688118	65.32554791	71.17523603

	14.29140445	85.26500639	70.97360194

	58.7	129.5	70.8

	11.97648788	82.61082938	70.6343415,

	14.30073607	84.68236855	70.381632481

	7.305502846	62.96737927	70.27288212

	15.16614831	84.8190644	69.65291612

	38.57217917	107.8998073	69.32762815

	38.64682418	107.8504978	69.20367362

	21.28742515	90.20742087	68.91999572

	31.28187691	100.1843318	68.90245488

	19.37221111	87.66541823	68.29320712

	14.5	82.8	68.3

	34.13126397	102.3629331	68.23166909

	11.72800505	79.87789988	68.14989482

	39.1	107.0	67.9

	25.28012412	92.88964225	67.60951814

	34.53258845	102.0162884	67.48369999

	23.0	89.9	66.9

	37.92480367	104.5573433	66.6325396

	43.2	109.5	66.3

	30.47645315	96.72727273	66.25081958

	34.54623163	100.760843	66.2146114

	23.45468053	89.61072441	66.15604388

	24.12504492	90.1231625	65.99811758

	27.16644285	93.0177803	65.85133746

	−8.097006083	57.6845011	65.78150718

	66.13604597	131.2029473	65.06690133

	11.19902121	76.15107324	64.95205204

	4.577793748	69.52721494	64.94942119

	18.95094399	83.66485345	64.71390946

	26.7	91.4	64.7

	34.3965106	99.00834642	64.61183582

	31.16639478	95.42028511	64.25389033

	32.90443509	97.09434568	64.18991059

	36.11902501	100.2785294	64.15950436

	35.72624681	99.74101397	64.01476715

	21.78361457	85.37461774	63.59100317

	39.7488359	103.3154122	63.56657629

	41.28528975	104.7348973	63.44960756

	43.51306119	106.9095962	63.39653504

	18.57176712	81.71632703	63.14455991

	29.27084059	92.34063996	63.06979937

	31.39551493	94.41842001	63.02290508

	48.21516581	111.214653	62.99948715

	27.71898883	90.70584478	62.98685595

	38.47471452	101.4501065	62.97539199

	−19.61126884	43.27239348	62.88366232

	6.012957705	68.85183202	62.83887431

	29.45492662	92.21556886	62.76064224

	35.6	98.3	62.7

	43.7012494	106.4084449	62.70719545

	40.93873164	103.0201067	62.08137505

	31.21264846	93.01166131	61.79901285

	39.52157023	101.2560945	61.73452431

	59.441744	120.9256794	61.48393538

	25.38058602	86.7447645	61.36417848

	39.32183657	100.3628503	61.04101373

	18.43595701	79.39308398	60.95712697

	−29.64270278	31.23996145	60.88266423

	27.27621091	88.11755764	60.84134673

	37.6	98.3	60.7

	4.673280876	65.02894576	60.35566489

	41.8167411	102.1683264	60.35158527

	39.93161377	99.39343581	59.46182205

	41.01271009	100.3606236	59.34791354

	47.18965126	106.5320264	59.34237511

	36.55154869	95.64034877	59.08880009

	41.78912826	100.8274721	59.03834381

	34.66750489	93.68924174	59.02173685

	18.74037573	77.59057823	58.85020251

	22.81374655	81.47543659	58.66169004

	39.52194519	98.09873249	58.5767873

	39.11594696	97.63720151	58.52125455

	30.40891164	88.85677858	58.44786694

	25.20612485	83.4987795	58.29265464

	43.16379248	101.2275149	58.06372239

	31.4290114	89.23693465	57.80792326

	7.609675481	65.35257732	57.74290184

	38.17542436	95.91685226	57.74142791

	27.92957859	85.64814815	57.71856956

	48.94267421	106.2615101	57.31883592

	32.32116549	89.4407446	57.11957911

	38.73239121	95.62561095	56.89271974

	45.19897498	102.0166733	56.81769831

	35.39582849	92.03372469	56.6378962

	34.63356974	90.94954311	56.31597337

	44.3733406	100.6715454	56.29820482

	41.985733	98.20470972	56.21897672

	45.61615856	101.6646949	56.04853639

	41.13775626	97.06777083	55.93001457

	7.821811681	63.5443038	55.72249212

	45.56074766	101.2544661	55.69371839

	43.76933274	99.37348265	55.60414991

	43.36958596	98.96808255	55.5984966

	35.11114267	90.69859962	55.58745694

	29.48940031	85.03813193	55.54873162

	35.03258269	90.44736221	55.41477952

	55.47976701	110.818343	55.3385760

	38.04746419	93.34466638	55.29720219

	40.13238539	95.37388609	55.2415007

	44.19099554:	99.42563929	55.23464375

	33.24656324	87.76949553	54.52293229

	36.15465782	91.34577213	55.19111431

	27.2754491	82.27419222	54.99874311

	36.59699818	91.44689379	54.84989561

	37.48100881	92.20830691	54.7272981

	19.17808219	73.82692962	54.64884742

	21.54074074	76.08572124	54.5449805

	45.20486556	99.55872914	54.35386358

	32.60195759	86.63771915	54.03576157

	28.03761445	82.01902665	53.9814122

	30.81305821	84.78776478	53.97470658

	41.22497055	95.08543531	53.88046476

	42.82815987	96.57675493	53.74859506

	52.01193335	105.6743612	53.66244278

	43.85063378	97.46473998	53.61410621

	39.74584291	93.29913695	53.55329404

	41.15745598	94.72268477	53.56522879

	−19.8129509	33.73781755	53.55076845

	13.28219273	66.62503346	53.34284073

	40.42061339	93.71157747	53.29096408

	50.38587118	103.6178964	53.23202524

	45.37762426	98.52069172	53.14306746

	36.25704957	89.38134811	53.12429854

	30.70619785	83.66680278	52.96060492

	55.56846133	108.4823958	52.91393446

	36.80576864	89.70132202	52.89555338

	38.82044965	91.59237753	52.77192788

	50.81668419	103.4121817	52.59549746

	46.42363385	99.00409172	52.58045787

	69.98574323!	122.2854715	52.29972831

	25.26217665	77.54573418	52.28355753

	39.96352925	92.21643287	52.25290362

	47.00574838	99.25113873	52.24539035

	53.4905597	105.6295695	52.13900976

	49.44050318	101.5763783	52.13587515

	39.83535868	91.73339804	51.89803936

	54.02808574	105.7595451	51.73145935

	51.20524073	102.9357651	51.73052441

	43.22472716	94.84355045	51.61882329

	42.5929832	94.16497422	51.57199103

	32.55627595	83.96631306	51.41003711

	47.31068916	98.28460368	50.97391452

	48.55678968	97.50512926	50.94833958

	34.10555385	85.00081606	50.89526221

	30.59011861	81.34023006	50.75011146

	55.74433657	106.4705403	50.72620373

	44.76047904	95.3640196	50.60354046

	−20.05671367	30.41972806	50.47644174

	35.60617193	85.8825454	50.27637346

	57.07388105	107.3051263	50.2312452

	48.7076967	98.89474361	50.1870469

	56.5514328	106.3303342	49.77890139

	50.4177415	100.1803601	49.76261858

	46.79236779	96.49484536	49.70247757

	56.60157162	106.2747212	49.67314961

	33.00999412	82.65729799	49.64730387

	29.33477056	78.76829966	49.43352911

	33.27874504	82.81218664	49.33344159

	50.5499649	99.82531364	49.275348751

	30.48780488	79.68386424	49.19605936!

	47.95352324	96.90361633	48.95009309

	35.81991695:	84.74370394	48.923786139

	47.9673093	96.80006481	48.8327555

	33.22160149	81.90084605	48.67924456

	48.95344507	97.58836088	48.63491581

	57.44228744!	105.7704113	48.32812389

	44.25172198	92.47479302	48.22307104

	44.23800949	92.39348471	48.15547522

	215.6015433	263.7374061	48.13586273

	56.33127545	104.4315992	48.10032378

	55.14812663	103.2306124	48.08248577

	64.63766028	112.7047864	48.0671261

	44.40577958	92.47084671	48.06506715

	51.18862475	99.22340759	48.03478284

	20.34336068	68.23874445	47.89538377

	44.3557943	92.23836973	47.88257544

	67.95159426	115.7456877	47.79409342

	55.76098501	103.5302403	47.76925533

	48.75160508	96.45841953	47.70681445

	48.26958106	95.97238934	47.70280828

	69.86140798	117.5434343	47.68202636

	48.52722404	96.19903793	47.67181389

	40.64114261	88.27679138	47.63564887

	43.06535747	90.61530929	47.54995182

	40.42192793	87.79749734	47.37556941

	62.71844661	110.0825659	47.36411929

	58.50862999	105.8574397	47.34880968

	34.9335249	82.24076281	47.30723784

	53.71064468	101.0010865	47.29044177

	28.42089641	75.68202804	47.26113163

	47.02449336	94.14723747	47.12274411

	55.0937101	102.2099448	47.11623465

	30.48240503	77.54573418	47.06332914

	51.13822161	98.19719754	47.05897593

	65.41604755	112.4344762	47.01842869

	48.322054	95.33022533	47.00817133

	35.82692457	82.4672171	46.64029252

	45.64428312	92.1013059	46.45702277

	49.68408533	96.06979643	46.38571109

	48.65415987	95.02703588	46.37287601

	58.11789038	104.3981674	46.28027705

	40.50995892	86.74650699	46.23654806

	44.35757282	90.48873778	46.13116496

	47.01730419	93.0593376	46.04203341

	63.36025402	109.3342199	45.97396591

	40.75591985	86.72661643	45.97069857

	66.09053804	111.9999168	45.90937874

	69.53461354	115.1985743	45.66396079

	56.10428305	101.763264	45.65898096

	42.83942002	88.37759042	45.5381704

	50.06136852	95.57695446	45.51558595

	52.76268116	98.25183684	45.48915568

	53.00666405	98.46315619	45.45649214

	47.98902391	93.41583758	45.42681367

	58.33277892	103.7511722	45.41839332

	55.45434348	100.8550361	45.4006926

	68.79611916	114.1804937	45.38437457

	47.68581216	92.92784163	45.24202948

	37.60579356	82.80346821	45.19767465

	49.80397458	94.9926722	45.18869762

	52.42631325	97.49812983	45.07181658

TABLE 1-O

Structure	Structure

TABLE 1-P

		MCL-1 %	BCL-XL %	Spec
Bioactive	Structure	Bound	Bound	Values

Myricetin		34.13126397	102.3629331	68.21166909

Quercetin		16.68871081	105.3416001	88.65288929

Tyrphostin 47		34.54623163	100.760843	66.2146114

Manoalide		35.01128141	106.8345939	71.8233125

U73122		56.60157162	106.2747212	49.67314961

Baicailen		10.32290702	104.1661092	93.84320213

Dyclonine		1.259544221	90.57802572	89.3184815

Bithionol		27.20036677	100.4228001	73.22243335

Gossypol		3.955080904	101.0243434	97.0692625

Hexa- chloro- phene		41.01271009	100.3606236	59.34791354

Celastrol		32.90443509	97.09434568	64.18991059

Tannic Acid		15.93536133	98.2573418	82.32198048

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Claims

1-36. (canceled)

37. A compound of the formula (A):

wherein

n is an integer from 0-4;

q is an integer from 0-1;

X is ═O or —O—R³;

R¹is substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, —S—R^2a, —SO₂—R^2a;

R²is hydrogen, halogen, —NH—R^2a, —NH—R^2a, —S—CN, —S—R^2a, —S—CH₂—R^2aor —SO₂—R^2a;

each occurrence of R^2ais independently C₁-C₈alkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl;

R³is hydrogen, C₁-C₈alkyl substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl; and

each occurrence of Z and Z′ is independently halogen, hydroxyl, C₁-C₈alkyl, C₂-C₈alkenyl, C₂-C₈alkynyl, or C₁-C₆alkoxy, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, substituted or unsubstituted cycloalkyl, or substituted or unsubstituted heterocycloalkyl.

38. The compound of claim 37, wherein n is 0.

39. The compound of claim 37, wherein q is 0.

40. The compound of claim 37, wherein X is ═O.

41. The compound of claim 37, wherein R¹is —SO₂—R^2a, in which R^2ais substituted aryl.

42. The compound of claim 41, wherein R^2ais 4-methylphenyl.

43. The compound of claim 37, wherein R²is —S—R^2ain which R^2ais unsubstituted heteroaryl.

44. The compound of claim 43, wherein R^2ais 1,2,4-triazolyl.

45. The compound of claim 37, wherein the compound is

46. A pharmaceutical composition comprising the compound of claim 37 or a physiologically acceptable salt, solvate, hydrate or stereoisomer thereof and a pharmaceutically acceptable diluent or carrier.

47. A method of selectively modulating MCL-1 in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating MCL-1 in the cell.

48. A method for modulating apoptotic cell death in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating apoptotic cell death in the cell.

49. A method for modulating autophagy in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating autophagy in the cell.

50. A method for modulating necrotic cell death in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating necrotic cell death in the cell.

51. A method for modulating metabolism in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating energy production and consumption to effect cell viability in the cell.

52. A method for modulating cell division in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating proliferation in the cell.

53. A method for modulating transcription in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating transcription in the cell.

54. A method for modulating RNA processing in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating RNA processing in the cell.

55. A method for modulating differentiation in a stem or progenitor cell, comprising contacting the stem or progenitor cell with one or more compounds of claim 37, thereby regulating the lineage and phenotype in the cell.

56. A method for modulating multimerization of MCL-1 in a cell, comprising contacting the cell with one or more compounds of claim 37, thereby regulating multimerization of MCL-1 in the cell.

57. A method of treating a hyperproliferative disorder in a mammal, comprising administering to the mammal in need thereof a therapeutically effective amount of one or more compounds of claim 37.

58. The method of claim 57, wherein the hyperproliferative disorder is cancer.

59. A method of treating an angiogenesis disorder in a mammal, comprising administering to the mammal in need thereof a therapeutically effective amount of one or more compounds of claim 37.

60. A method of treating an inflammatory disease or disorder in a mammal, comprising administering to the mammal in need thereof a therapeutically effective amount of one or more compounds of claim 37.

61. A method of treating an infectious disease or disorder in a mammal, comprising administering to the mammal in need thereof a therapeutically effective amount of one or more compounds of claim 37.

62. A method of treating a cell cycle regulation disease or disorder in a mammal, comprising administering to the mammal in need thereof a therapeutically effective amount of one or more compounds of claim 37.

63. A method of treating an autophagy regulation or disorder in a mammal, comprising administering to the mammal in need thereof a therapeutically effective amount of one or more compounds of claim 37.

64. A method of treating an autoimmune disease or disorder in a mammal, comprising administering to the mammal in need thereof a therapeutically effective amount of one or more compounds of claim 37.